library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
## enrichment tool for interpreting omics data. The Innovation. 2021,
## 2(3):100141
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:clusterProfiler':
## 
##     rename
## The following object is masked from 'package:utils':
## 
##     findMatches
## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
## The following object is masked from 'package:clusterProfiler':
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##     slice
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##     windows
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:clusterProfiler':
## 
##     select
## 
library(stringr)
library(ggplot2)

The results here are deprecated in favor of FABIA variables selected using thres_L (extractBic()).

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

Due to long computational time to obtain gene names for microRNA and to execute pathway analysis,

pathway analysis will only be done for 1, 2, 3, 5 and 10-bicluster FABIA.

results.fabia = readRDS("data/sel_features/results_fabia_top_5_percent.rds")
sel.features = results.fabia[1:5]
sel.features
## $`1bc`
## $`1bc`$bicluster1
##      G6PD.RPPA      TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197 
##     -0.5664688     -0.5495991      0.7662391      0.6351004      0.6196432 
##    hsa-mir-127    hsa-mir-134    hsa-mir-136    hsa-mir-154    hsa-mir-323 
##      0.5556598      0.5553999      0.5555263      0.5772620      0.5936458 
##   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 
##      0.6038210      0.6858061      0.6838698      0.5848124      0.5874765 
## hsa-mir-376a-2   hsa-mir-376c    hsa-mir-377    hsa-mir-380    hsa-mir-382 
##      0.6262681      0.5575709      0.6136535      0.6782381      0.5608688 
##    hsa-mir-409    hsa-mir-411    hsa-mir-433    hsa-mir-485   hsa-mir-487a 
##      0.5577673      0.6712205      0.6026199      0.6385659      0.7267015 
##    hsa-mir-494    hsa-mir-496    hsa-mir-541    hsa-mir-543    hsa-mir-654 
##      0.6434824      0.5717559      0.6543345      0.6088287      0.5726739 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##      0.6905221      0.8365020      0.5754425      0.6625089      0.6163359 
##    hsa-mir-889 
##      0.5576494 
## 
## 
## $`2bc`
## $`2bc`$bicluster2
##      G6PD.RPPA      FASN.RPPA      TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 
##     -0.4947514      0.5768981     -0.5100910      0.5594705      0.4696187 
##   hsa-mir-1197    hsa-mir-323  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 
##      0.4989459      0.4716776      0.5510674      0.6231958      0.4669418 
## hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-377    hsa-mir-380    hsa-mir-411 
##      0.4945849      0.4993865      0.4885167      0.5553450      0.4690795 
##    hsa-mir-433    hsa-mir-466   hsa-mir-487a    hsa-mir-494    hsa-mir-506 
##      0.4727682     -0.4874996      0.5465899      0.4714333     -0.5175712 
##    hsa-mir-507    hsa-mir-508    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 
##     -0.5847532     -0.5014800     -0.7000950     -0.5146970     -0.5416414 
##   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3 
##     -0.4808000     -0.4772028     -0.5008222     -0.5045772     -0.5027646 
##    hsa-mir-541    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668 
##      0.5403953      0.5126972      0.6667496      0.5263446      0.5101166 
##    hsa-mir-770 
##      0.5519820 
## 
## $`2bc`$bicluster1
##       FN1.R2Gn    CTNNB1.R2Gn     CCND1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 
##     -0.4511588     -0.4925327     -0.4626447      0.5297352      0.4314716 
##   hsa-mir-135b    hsa-mir-206   hsa-mir-3166 hsa-mir-3199-1   hsa-mir-323b 
##     -0.3906779     -0.4583481     -0.4034852      0.4173045      0.3852651 
##  hsa-mir-329-1 hsa-mir-376a-2    hsa-mir-380   hsa-mir-3923    hsa-mir-411 
##      0.4048227      0.3728961      0.3843573     -0.3936415      0.4946514 
##    hsa-mir-433    hsa-mir-485   hsa-mir-487a    hsa-mir-494    hsa-mir-506 
##      0.3724767      0.4700524      0.4803354      0.4429761      0.4240878 
##    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2  hsa-mir-509-3 
##      0.5126687      0.4074888      0.4327297      0.4354988      0.4239098 
##    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2  hsa-mir-514-1  hsa-mir-514-2 
##      0.5448665      0.3938817      0.4365787      0.4445967      0.4491853 
##  hsa-mir-514-3   hsa-mir-514b    hsa-mir-543    hsa-mir-655    hsa-mir-656 
##      0.4515958      0.4196900      0.4407581      0.4666229      0.4984523 
##    hsa-mir-668 
##      0.4212441 
## 
## 
## $`3bc`
## $`3bc`$bicluster2
##      G6PD.RPPA      FASN.RPPA      TTF1.RPPA      TGM2.R2Gn    SQSTM1.R2Gn 
##     -0.6514624      0.8737953     -0.6094855     -0.7011726     -0.6331867 
## hsa-mir-1185-1   hsa-mir-1197  hsa-mir-329-1  hsa-mir-329-2 hsa-mir-376a-1 
##      0.7013345      0.6522884      0.7064830      0.8107564      0.6354677 
## hsa-mir-376a-2    hsa-mir-377    hsa-mir-380    hsa-mir-466   hsa-mir-487a 
##      0.6617729      0.6303237      0.7212568     -0.6553467      0.7015375 
##    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2 
##     -0.7206063     -0.8075650     -0.6905181     -0.6306047     -0.6340692 
##  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b 
##     -0.6404349     -0.9915946     -0.7202971     -0.7574027     -0.6739789 
##   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3    hsa-mir-541 
##     -0.6583085     -0.7000274     -0.7049369     -0.7023947      0.7012658 
##    hsa-mir-605    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668 
##     -0.6444571      0.6524373      0.8623823      0.6826397      0.6457786 
##    hsa-mir-770 
##      0.7249692 
## 
## $`3bc`$bicluster3
##     GATA3.RPPA    IGFBP2.R2Gn       FN1.R2Gn    CTNNB1.R2Gn     CCND1.R2Gn 
##     -0.9248231     -0.6582546     -0.8641139     -0.9724582     -0.9043804 
## hsa-mir-1185-1  hsa-mir-124-3   hsa-mir-135b    hsa-mir-206   hsa-mir-2114 
##      0.6907430     -0.7375579     -0.6885645     -0.8045228      0.9326673 
##   hsa-mir-3166 hsa-mir-3199-1   hsa-mir-3655   hsa-mir-3923 hsa-mir-3926-2 
##     -0.7932514      0.8070724      0.7332915     -0.7798807      0.7178644 
##    hsa-mir-411    hsa-mir-429    hsa-mir-485   hsa-mir-487a    hsa-mir-506 
##      0.6875457     -0.6234259      0.6667901      0.6462570      1.0799827 
##    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2  hsa-mir-509-3 
##      1.3110639      1.0634858      1.1021953      1.1088305      1.0805202 
##    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c 
##      1.3487461      1.0030912      1.1041617      0.9312010      0.9159748 
##  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b    hsa-mir-582 
##      1.1088941      1.1209338      1.1254595      1.0572493     -0.6426409 
##    hsa-mir-656 
##      0.6249114 
## 
## $`3bc`$bicluster1
##    CTNNB1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197    hsa-mir-127 
##     -0.9033705      1.3503645      1.1107468      0.9529190      0.8771463 
##    hsa-mir-134    hsa-mir-136    hsa-mir-154    hsa-mir-206    hsa-mir-299 
##      0.8552275      0.8799115      0.9404601     -0.9422025      0.8557165 
##    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 
##      0.9517043      1.0090382      1.0896878      0.9268612      0.9256967 
## hsa-mir-376a-1 hsa-mir-376a-2   hsa-mir-376c    hsa-mir-377    hsa-mir-380 
##      0.8889023      0.9533043      0.8807044      0.9724277      1.0380931 
##    hsa-mir-382    hsa-mir-409    hsa-mir-411    hsa-mir-433    hsa-mir-485 
##      0.9003822      0.8873264      1.2199026      1.0121041      1.1513445 
##   hsa-mir-487a    hsa-mir-494    hsa-mir-496   hsa-mir-517a    hsa-mir-541 
##      1.2182208      1.0982661      0.9103087     -0.9189714      0.9954855 
##    hsa-mir-543    hsa-mir-654    hsa-mir-655    hsa-mir-656    hsa-mir-668 
##      1.0942886      0.9080437      1.1825263      1.3173936      1.1096351 
##    hsa-mir-889 
##      0.8914403 
## 
## 
## $`5bc`
## $`5bc`$bicluster2
##      G6PD.RPPA      FASN.RPPA      TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 
##      -1.223677       1.217596      -1.271622       1.570247       1.294725 
##   hsa-mir-1197    hsa-mir-127    hsa-mir-134    hsa-mir-154    hsa-mir-323 
##       1.337937       1.173178       1.199352       1.210786       1.245608 
##   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 
##       1.253850       1.433422       1.445291       1.236783       1.228026 
## hsa-mir-376a-2   hsa-mir-376c    hsa-mir-377    hsa-mir-380    hsa-mir-382 
##       1.388361       1.185418       1.297923       1.449953       1.180177 
##    hsa-mir-409    hsa-mir-411    hsa-mir-433    hsa-mir-485   hsa-mir-487a 
##       1.179492       1.389500       1.221530       1.337356       1.538557 
##    hsa-mir-494    hsa-mir-496    hsa-mir-541    hsa-mir-543    hsa-mir-654 
##       1.370792       1.184541       1.397750       1.264016       1.197898 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##       1.446290       1.774240       1.209625       1.367780       1.329506 
##    hsa-mir-889 
##       1.170309 
## 
## $`5bc`$bicluster5
##     RBM15.RPPA     GATA3.RPPA      FASN.RPPA       VHL.RPPA       FN1.R2Gn 
##      0.7184612      0.6924899      0.7530785     -0.7024914      0.7782749 
##      CDH2.R2Gn     GATA3.R2Gn    CTNNB1.R2Gn     CCND1.R2Gn  hsa-mir-124-3 
##      0.6767999      0.7291869      0.9789055      0.9398745      0.7354031 
##   hsa-mir-1258   hsa-mir-135b    hsa-mir-139    hsa-mir-206   hsa-mir-2114 
##     -0.8778078      0.7789183      0.6835076      0.7065935     -0.9474872 
##   hsa-mir-3166 hsa-mir-3199-1   hsa-mir-3655   hsa-mir-3923 hsa-mir-3926-2 
##      0.8217578     -0.8002071     -0.7022664      0.7653353     -0.8642790 
##    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2 
##     -1.2810821     -1.5268068     -1.2511387     -1.2461806     -1.2536204 
##  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b 
##     -1.2361909     -1.6619289     -1.2442761     -1.3369888     -1.1415689 
##   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b 
##     -1.1019043     -1.2999527     -1.3123096     -1.3144639     -1.2016029 
##    hsa-mir-605 
##     -0.7440529 
## 
## $`5bc`$bicluster1
##      FASN.RPPA hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197    hsa-mir-323 
##       1.117653       1.290131       1.071205       1.123461       1.077405 
##  hsa-mir-329-1  hsa-mir-329-2 hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-377 
##       1.241555       1.415258       1.148375       1.098217       1.078513 
##    hsa-mir-380    hsa-mir-431    hsa-mir-432    hsa-mir-433    hsa-mir-466 
##       1.257586       1.085488       1.091955       1.138532      -1.158672 
##   hsa-mir-487a    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1 
##       1.210012      -1.203164      -1.357510      -1.171702      -1.095243 
##  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 
##      -1.100937      -1.100505      -1.580255      -1.157794      -1.239173 
##   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3 
##      -1.094598      -1.108947      -1.164477      -1.173792      -1.171018 
##    hsa-mir-541    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668 
##       1.245527       1.142226       1.481162       1.187346       1.193894 
##    hsa-mir-770 
##       1.237206 
## 
## $`5bc`$bicluster4
##      G6PD.RPPA     GATA3.RPPA    IGFBP2.R2Gn       FN1.R2Gn     CCND1.R2Gn 
##     -0.8874401     -0.7115765     -0.7458151     -0.9565017     -0.8364112 
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1269   hsa-mir-135b    hsa-mir-206 
##      0.9376338      0.7793299     -0.8862766     -0.6839028     -0.7246469 
##   hsa-mir-2114   hsa-mir-3166  hsa-mir-329-1   hsa-mir-3655    hsa-mir-377 
##      0.7511895     -0.6856088      0.6745780      0.6822197      0.7118407 
##   hsa-mir-3923    hsa-mir-411    hsa-mir-429    hsa-mir-485   hsa-mir-487a 
##     -0.9393513      0.8631381     -0.6732284      0.8206766      0.8626403 
##    hsa-mir-494    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1 
##      0.7885223      0.7366205      0.8805492      0.6910378      0.7414954 
##  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-2  hsa-mir-514-1 
##      0.7465243      0.7250601      1.0051334      0.7350518      0.7706746 
##  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b    hsa-mir-543    hsa-mir-655 
##      0.7793074      0.7834490      0.7402679      0.7556145      0.8555369 
##    hsa-mir-656 
##      0.8747549 
## 
## $`5bc`$bicluster3
##    CTNNB1.R2Gn      TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197 
##     -0.7258220     -0.9917658      0.9119355      0.8179147      0.7677908 
##    hsa-mir-206    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2 
##     -0.7216070      0.7241902      0.7383052      0.9301956      0.8555830 
##    hsa-mir-370 hsa-mir-376a-1   hsa-mir-376c    hsa-mir-377    hsa-mir-380 
##      0.7268798      0.7067193      0.6981417      0.7398770      0.7912598 
##    hsa-mir-409    hsa-mir-411    hsa-mir-433    hsa-mir-485   hsa-mir-487a 
##      0.6927454      0.8515268      0.7315438      0.7494611      0.8980823 
##    hsa-mir-494 hsa-mir-516a-1 hsa-mir-516a-2 hsa-mir-516b-1   hsa-mir-517a 
##      0.7818349     -1.0238960     -0.8652304     -0.8930039     -1.1226980 
##   hsa-mir-518b hsa-mir-519a-2   hsa-mir-520a    hsa-mir-541    hsa-mir-543 
##     -0.9249284     -0.7535023     -0.7649585      0.8239600      0.7132918 
##    hsa-mir-654    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668 
##      0.7079798      0.8520211      1.0533879      0.6944180      0.8401613 
##    hsa-mir-770 
##      0.7400861 
## 
## 
## $`10bc`
## $`10bc`$bicluster9
##      G6PD.RPPA      FASN.RPPA      TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 
##      -1.462745       1.408663      -1.528343       1.630926       1.387648 
##   hsa-mir-1197    hsa-mir-127    hsa-mir-134    hsa-mir-136    hsa-mir-154 
##       1.293736       1.266737       1.301764       1.287702       1.306299 
##    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 
##       1.312769       1.320481       1.522231       1.652729       1.340504 
## hsa-mir-376a-1 hsa-mir-376a-2   hsa-mir-376c    hsa-mir-377    hsa-mir-380 
##       1.279101       1.392779       1.253179       1.412011       1.519219 
##    hsa-mir-382    hsa-mir-409    hsa-mir-411    hsa-mir-485   hsa-mir-487a 
##       1.253564       1.259344       1.490102       1.379905       1.629246 
##    hsa-mir-494    hsa-mir-496    hsa-mir-541    hsa-mir-543    hsa-mir-654 
##       1.419933       1.258245       1.372309       1.283927       1.297765 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##       1.588696       1.894492       1.422869       1.335580       1.445396 
##    hsa-mir-876 
##      -1.251928 
## 
## $`10bc`$bicluster10
##      FASN.RPPA      TTF1.RPPA       VHL.RPPA    IGFBP2.R2Gn      FASN.R2Gn 
##     -1.5274105      0.9069167      0.8539464     -0.8755194     -0.8902463 
##    CTNNB1.R2Gn    PIK3R1.R2Gn   hsa-mir-1193   hsa-mir-1258   hsa-mir-2114 
##     -0.8664015      0.8603335     -0.8257255      1.1115348      0.9960010 
##  hsa-mir-329-2    hsa-mir-380   hsa-mir-3909   hsa-mir-3922 hsa-mir-3926-2 
##     -1.1514295     -0.8568947      0.8736193      0.9005470      0.9053655 
##    hsa-mir-466    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1 
##      1.2096588      1.4877862      1.6584772      1.4428013      1.3927785 
##  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 
##      1.3999859      1.3987535      1.9970228      1.4671548      1.5612417 
##   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3 
##      1.3697259      1.3370295      1.4764641      1.4873631      1.4849702 
##   hsa-mir-514b    hsa-mir-605    hsa-mir-656    hsa-mir-665    hsa-mir-770 
##      1.2816265      1.1618128     -1.0122797     -0.9011850     -0.9453659 
##    hsa-mir-876 
##      0.8334968 
## 
## $`10bc`$bicluster7
##     GATA3.RPPA       FN1.R2Gn     GATA3.R2Gn    CTNNB1.R2Gn     CCND1.R2Gn 
##      0.8045924      1.5105720      0.8053707      0.7888432      1.0074275 
## hsa-mir-1185-1   hsa-mir-135b    hsa-mir-206   hsa-mir-2114    hsa-mir-296 
##     -0.8852070      0.9636991      0.8609145     -1.0739371     -0.8379147 
##   hsa-mir-3166 hsa-mir-3199-1 hsa-mir-320c-2   hsa-mir-3655   hsa-mir-3923 
##      0.8709674     -0.8448901     -0.7740326     -0.8200618      1.2458162 
## hsa-mir-3926-2    hsa-mir-411    hsa-mir-429    hsa-mir-485   hsa-mir-487a 
##     -0.7670181     -0.8065099      0.8136113     -0.7966192     -0.7572892 
##    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2 
##     -1.1966336     -1.5059972     -1.1635007     -1.1993246     -1.2090071 
##  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b 
##     -1.1840188     -1.5948701     -1.1167460     -1.2067379     -1.0652999 
##   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b 
##     -1.0159501     -1.2219215     -1.2360464     -1.2408427     -1.1833782 
##    hsa-mir-656 
##     -0.7860848 
## 
## $`10bc`$bicluster2
##      G6PD.RPPA hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197    hsa-mir-127 
##      -1.032402       1.572284       1.274336       1.277146       1.069279 
##    hsa-mir-134    hsa-mir-136    hsa-mir-154    hsa-mir-299    hsa-mir-323 
##       1.081196       1.050773       1.128018       1.039129       1.160717 
##   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 
##       1.194810       1.316845       1.147179       1.128664       1.125214 
## hsa-mir-376a-2   hsa-mir-376c    hsa-mir-377    hsa-mir-379    hsa-mir-380 
##       1.278186       1.088131       1.201200       1.025437       1.307862 
##    hsa-mir-382    hsa-mir-409    hsa-mir-411    hsa-mir-433    hsa-mir-485 
##       1.105750       1.081776       1.351776       1.182958       1.336577 
##   hsa-mir-487a    hsa-mir-494    hsa-mir-496    hsa-mir-541    hsa-mir-543 
##       1.462340       1.325635       1.103873       1.310411       1.277806 
##    hsa-mir-654    hsa-mir-655    hsa-mir-656    hsa-mir-668    hsa-mir-770 
##       1.095603       1.340141       1.681121       1.375431       1.131574 
##    hsa-mir-889 
##       1.078448 
## 
## $`10bc`$bicluster1
##       FN1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197    hsa-mir-127 
##     -0.9547080      1.2875673      1.0640023      0.9647186      0.9416451 
##    hsa-mir-134    hsa-mir-136    hsa-mir-154    hsa-mir-299    hsa-mir-323 
##      0.9477569      0.9450738      0.9481687      0.8898955      0.9558071 
##   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 
##      1.0119887      1.0574270      1.0611295      0.9593036      0.9414308 
## hsa-mir-376a-2   hsa-mir-376c    hsa-mir-377    hsa-mir-379    hsa-mir-380 
##      1.0470675      0.8943005      0.9395190      0.8850704      1.1203452 
##    hsa-mir-382    hsa-mir-409    hsa-mir-411    hsa-mir-433    hsa-mir-485 
##      0.8992530      0.9242129      1.1144084      1.0782266      1.0886604 
##   hsa-mir-487a    hsa-mir-494    hsa-mir-496    hsa-mir-541    hsa-mir-543 
##      1.2093248      1.0174403      0.9098792      1.0520097      1.0151944 
##    hsa-mir-654    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668 
##      0.9399797      1.1057531      1.3345000      0.9436418      1.0677259 
##    hsa-mir-770 
##      0.9978195 
## 
## $`10bc`$bicluster3
##      FASN.RPPA      TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197 
##      0.5760663     -0.7815945      0.6713936      0.6070342      0.6275874 
##   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2 hsa-mir-376a-1    hsa-mir-380 
##      0.5725844      0.7096430      0.7284656      0.5902027      0.6004218 
##    hsa-mir-433   hsa-mir-487a    hsa-mir-506    hsa-mir-507    hsa-mir-508 
##      0.5975042      0.6349316     -0.6827509     -0.7432906     -0.7058996 
##  hsa-mir-509-1  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 
##     -0.6336533     -0.6342927     -0.6313652     -0.9944091     -0.7219759 
## hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2 
##     -0.7453797     -0.6549005     -0.6759318     -0.6560391     -0.6623585 
##  hsa-mir-514-3   hsa-mir-514b hsa-mir-516a-1 hsa-mir-516a-2 hsa-mir-516b-1 
##     -0.6561356     -0.6772861     -0.5805846     -0.5930698     -0.7750374 
##   hsa-mir-517a   hsa-mir-518b    hsa-mir-541    hsa-mir-656    hsa-mir-668 
##     -0.8073668     -0.8075451      0.6592196      0.8191651      0.6652767 
##    hsa-mir-770 
##      0.6483303 
## 
## $`10bc`$bicluster8
##      G6PD.RPPA     ERBB3.R2Gn      TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 
##     -0.8578145      1.0985669     -0.7422173      1.0497708      0.8854318 
##   hsa-mir-1197    hsa-mir-136    hsa-mir-154    hsa-mir-323   hsa-mir-323b 
##      0.7948017      0.7426809      0.7654090      0.7785561      0.8043037 
##  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 
##      0.8900127      0.8349306      0.7575411      0.7445226      0.7800835 
##    hsa-mir-377    hsa-mir-380    hsa-mir-382    hsa-mir-409    hsa-mir-411 
##      0.8123670      0.8673392      0.7274808      0.7332409      0.8832058 
##    hsa-mir-433    hsa-mir-485   hsa-mir-487a   hsa-mir-487b    hsa-mir-494 
##      0.8246066      0.8393091      0.9210298      0.7299098      0.8012510 
##    hsa-mir-496   hsa-mir-517a    hsa-mir-541    hsa-mir-543    hsa-mir-654 
##      0.8134274     -0.9384336      0.8027538      0.8393921      0.7468551 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-770 
##      0.8661148      1.1191052      0.7904591      0.8699738      0.7341120 
##    hsa-mir-889 
##      0.7577327 
## 
## $`10bc`$bicluster6
##      G6PD.RPPA     RBM15.RPPA      FASN.RPPA       VHL.RPPA     GAPDH.RPPA 
##     -0.4822755      0.5284256      0.9751094     -0.4726870      0.5564764 
##      MSH6.RPPA      CDH2.R2Gn      EEF2.R2Gn    SQSTM1.R2Gn   hsa-mir-1193 
##      0.6367145      0.4771812      0.5311071     -0.4876945      0.5428938 
##  hsa-mir-124-3   hsa-mir-1258 hsa-mir-1270-1 hsa-mir-3926-2   hsa-mir-3934 
##      0.4920527     -0.6231183     -0.4797317     -0.4938113     -0.7307437 
##    hsa-mir-466    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1 
##     -0.7125538     -0.5317464     -0.4940167     -0.4834298     -0.4634957 
##  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 
##     -0.4639393     -0.4581791     -0.7708856     -0.5439687     -0.5910066 
##   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3 
##     -0.5158769     -0.4635426     -0.5332727     -0.5358638     -0.5331768 
##   hsa-mir-514b   hsa-mir-548v    hsa-mir-552    hsa-mir-592    hsa-mir-605 
##     -0.4597463     -0.5293097     -0.5151529     -0.4793774     -0.8211215 
##    hsa-mir-653 
##     -0.5537353 
## 
## $`10bc`$bicluster5
##      CDH2.R2Gn    CTNNB1.R2Gn     CCND1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 
##      0.4472989      0.5932909      0.3867946     -0.5737252     -0.4375696 
##   hsa-mir-1197   hsa-mir-1269    hsa-mir-127    hsa-mir-136    hsa-mir-154 
##     -0.3964926      0.4330842     -0.4016385     -0.3868483     -0.3950753 
##    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-370 
##     -0.4171626     -0.4575472     -0.4831626     -0.4377473     -0.3825449 
## hsa-mir-376a-1 hsa-mir-376a-2    hsa-mir-380    hsa-mir-381    hsa-mir-410 
##     -0.3840932     -0.4109170     -0.4545492     -0.3911366     -0.4196650 
##    hsa-mir-411    hsa-mir-432    hsa-mir-433    hsa-mir-485   hsa-mir-487a 
##     -0.5647757     -0.3986083     -0.5586840     -0.5123031     -0.4939001 
##    hsa-mir-488    hsa-mir-494    hsa-mir-495    hsa-mir-496    hsa-mir-541 
##      0.4141016     -0.4413336     -0.3912357     -0.3825438     -0.4612918 
##    hsa-mir-543    hsa-mir-552    hsa-mir-654    hsa-mir-655    hsa-mir-668 
##     -0.4811812     -0.4072452     -0.3864806     -0.5451296     -0.4855031 
##    hsa-mir-889 
##     -0.3910674 
## 
## $`10bc`$bicluster4
##      G6PD.RPPA       NF2.RPPA      G6PD.R2Gn      TFRC.R2Gn       PXN.R2Gn 
##     -0.8633667      0.3005225     -0.4510887     -0.3082843     -0.3541556 
##  hsa-mir-105-1  hsa-mir-105-2 hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1249 
##     -0.3371216     -0.3576975      0.4217317      0.3526467      0.4325660 
##   hsa-mir-1269    hsa-mir-134    hsa-mir-136   hsa-mir-216b    hsa-mir-217 
##     -0.4865206      0.3083781      0.3068420     -0.5211621     -0.3442703 
##  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-377    hsa-mir-380    hsa-mir-433 
##      0.3504894      0.3563077      0.3687179      0.3149718      0.3572780 
##    hsa-mir-483    hsa-mir-485   hsa-mir-487a    hsa-mir-494    hsa-mir-507 
##     -0.3707636      0.3006943      0.3939835      0.3356774     -0.3081056 
##    hsa-mir-543    hsa-mir-552    hsa-mir-577    hsa-mir-598    hsa-mir-655 
##      0.2896204     -0.2926853     -0.3540091     -0.2935015      0.3371770 
##    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-767    hsa-mir-770 
##      0.3617603      0.3529829      0.3320721     -0.3312544      0.3103354 
##    hsa-mir-876 
##     -0.2951831

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
  out = as.character(unique(out1))
  out
}
geneNames <- list("Factor1of1"= multiomics.to.GENES(names(sel.features$`1bc`$bicluster1)),
                  
                  "Factor1of2"= multiomics.to.GENES(names(sel.features$`2bc`$bicluster1)),
                  "Factor2of2"= multiomics.to.GENES(names(sel.features$`2bc`$bicluster2)),
                  
                  "Factor1of3"= multiomics.to.GENES(names(sel.features$`3bc`$bicluster1)),
                  "Factor2of3"= multiomics.to.GENES(names(sel.features$`3bc`$bicluster2)),
                  "Factor3of3"= multiomics.to.GENES(names(sel.features$`3bc`$bicluster3)),
                  
                  "Factor1of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster1)),
                  "Factor2of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster2)),
                  "Factor3of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster3)),
                  "Factor4of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster4)),
                  "Factor5of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster5)),
                  
                  "Factor1of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster1)),
                  "Factor2of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster2)),
                  "Factor3of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster3)),
                  "Factor4of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster4)),
                  "Factor5of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster5)),
                  "Factor6of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster6)),
                  "Factor7of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster7)),
                  "Factor8of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster8)),
                  "Factor9of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster9)),
                  "Factor10of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster10))
                  )
## Searching mirecords ...
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geneNames
## $Factor1of1
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "STAT5A" "CCND1"  "YAP1"   "MAPK1"  "ANLN"   "ITGA2"  "TGM2"   "G6PD"  
## 
## $Factor1of2
##  [1] "ESR1"   "MET"    "G6PD"   "BCL2"   "KRAS"   "CCND1"  "NOTCH3" "AKT1"  
##  [9] "IGF1R"  "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "PTEN"   "NRAS"  
## [17] "PTK2"   "ATM"    "YWHAZ"  "FOXO3"  "CHEK1"  "FN1"    "NCOA3"  "GAB2"  
## [25] "ITGA2"  "CTNNB1"
## 
## $Factor2of2
##  [1] "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "CCND1"  "PIK3R1" "CHEK1"  "IGF1R"  "SRSF1" 
## [17] "TUBA1B" "STAT5A" "NCOA3"  "GAB2"   "YAP1"   "MAPK1"  "ANLN"   "TGM2"  
## [25] "G6PD"   "FASN"  
## 
## $Factor1of3
##  [1] "ESR1"   "MET"    "G6PD"   "BCL2"   "KRAS"   "CCND1"  "NOTCH3" "AKT1"  
##  [9] "IGF1R"  "HSPA1A" "VHL"    "MTOR"   "MAPK8"  "PTEN"   "NRAS"   "PTK2"  
## [17] "ETS1"   "ATM"    "CDKN1A" "STAT5A" "FOXO3"  "CHEK1"  "FN1"    "ITGA2" 
## [25] "CTNNB1"
## 
## $Factor2of3
##  [1] "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "CCND1"  "PIK3R1" "CHEK1"  "IGF1R"  "SRSF1" 
## [17] "TUBA1B" "STAT5A" "NCOA3"  "GAB2"   "YAP1"   "MAPK1"  "ANLN"   "TGM2"  
## [25] "SQSTM1" "G6PD"   "FASN"   "TTF1"  
## 
## $Factor3of3
##  [1] "ESR1"    "MET"     "BAP1"    "ERRFI1"  "G6PD"    "BCL2"    "KRAS"   
##  [8] "CCND1"   "NOTCH3"  "AKT1"    "IGF1R"   "PTEN"    "CDKN1B"  "IRS1"   
## [15] "MYC"     "JUN"     "BCL2L11" "EZH2"    "SHC1"    "XIAP"    "ETS1"   
## [22] "MAPK8"   "ARID1A"  "BID"     "YWHAZ"   "FOXO3"   "CHEK1"   "FN1"    
## [29] "NCOA3"   "AXL"     "PTK2"    "CDKN1A"  "EGFR"    "CAV1"    "CASP3"  
## [36] "ANXA1"   "TFF1"    "STAT3"   "ASNS"    "FOXM1"   "IGFBP2"  "ITGA2"  
## [43] "RET"     "SQSTM1"  "CCNE2"   "GAB2"    "NDRG1"   "INPP4B"  "LCN2"   
## [50] "RAD50"   "CTNNB1"  "GATA3"  
## 
## $Factor1of5
##  [1] "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "CCND1"  "PIK3R1" "CHEK1"  "IGF1R"  "SRSF1" 
## [17] "TUBA1B" "STAT5A" "NCOA3"  "GAB2"   "YAP1"   "MAPK1"  "ANLN"   "FASN"  
## 
## $Factor2of5
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "STAT5A" "CCND1"  "YAP1"   "MAPK1"  "ANLN"   "ITGA2"  "TGM2"   "G6PD"  
## [25] "FASN"  
## 
## $Factor3of5
##  [1] "ESR1"   "MET"    "G6PD"   "BCL2"   "KRAS"   "CCND1"  "NOTCH3" "AKT1"  
##  [9] "IGF1R"  "MYH9"   "CDKN1A" "FOXO3"  "ATM"    "CASP8"  "MACC1"  "PTEN"  
## [17] "NRAS"   "PTK2"   "ETS1"   "STAT5A" "CHEK1"  "FN1"    "YAP1"   "MAPK1" 
## [25] "ANLN"   "ITGA2"  "CTNNB1" "TGM2"  
## 
## $Factor4of5
##  [1] "ESR1"    "MET"     "BAP1"    "ERRFI1"  "G6PD"    "BCL2"    "KRAS"   
##  [8] "CCND1"   "NOTCH3"  "AKT1"    "IGF1R"   "PTEN"    "CDKN1B"  "IRS1"   
## [15] "MYC"     "JUN"     "BCL2L11" "EZH2"    "SHC1"    "XIAP"    "ETS1"   
## [22] "MAPK8"   "ARID1A"  "BID"     "NRAS"    "PTK2"    "ATM"     "YWHAZ"  
## [29] "FOXO3"   "CHEK1"   "FN1"     "NCOA3"   "AXL"     "CDKN1A"  "EGFR"   
## [36] "CAV1"    "CASP3"   "ANXA1"   "TFF1"    "STAT3"   "ASNS"    "FOXM1"  
## [43] "IGFBP2"  "ITGA2"   "RET"     "SQSTM1"  "CCNE2"   "GAB2"    "NDRG1"  
## [50] "INPP4B"  "LCN2"    "RAD50"   "GATA3"  
## 
## $Factor5of5
##  [1] "ESR1"   "MET"    "G6PD"   "BCL2"   "KRAS"   "CCND1"  "NOTCH3" "AKT1"  
##  [9] "IGF1R"  "RB1"    "XIAP"   "ETS1"   "MAPK8"  "ARID1A" "BID"    "YWHAZ" 
## [17] "FOXO3"  "CHEK1"  "FN1"    "NCOA3"  "GAB2"   "CDH2"   "GATA3"  "CTNNB1"
## [25] "RBM15"  "FASN"   "VHL"   
## 
## $Factor1of10
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "STAT5A" "CCND1"  "YAP1"   "MAPK1"  "ANLN"   "ITGA2"  "FN1"   
## 
## $Factor2of10
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "PTEN"   "KRAS"   "NRAS"  
##  [9] "PTK2"   "ETS1"   "ATM"    "CDKN1A" "STAT5A" "ITGA2"  "G6PD"  
## 
## $Factor3of10
##  [1] "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "CDKN1A" "STAT5A" "NCOA3" 
##  [9] "GAB2"   "TGM2"   "FASN"  
## 
## $Factor4of10
##  [1] "ETS1"    "XIAP"    "MAPK8"   "ARID1A"  "BID"     "MYH9"    "CDKN1A" 
##  [8] "FOXO3"   "ATM"     "CASP8"   "MACC1"   "PTEN"    "KRAS"    "NRAS"   
## [15] "PTK2"    "PARP1"   "IGF1R"   "CCNE2"   "RAB25"   "EZH2"    "RAB11B" 
## [22] "NCOA3"   "GAB2"    "CCND1"   "YAP1"    "MAPK1"   "ANLN"    "ITGA2"  
## [29] "BCL2"    "MYC"     "CASP3"   "BCL2L11" "MSH6"    "PIK3CA"  "SRSF1"  
## [36] "MSH2"    "CDH1"    "CTNNB1"  "IGFBP2"  "PRKAA1"  "YWHAB"   "G6PD"   
## [43] "TFRC"    "PXN"     "NF2"    
## 
## $Factor5of10
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "PTEN"   "KRAS"   "NRAS"  
##  [9] "PTK2"   "ETS1"   "ATM"    "CDKN1A" "STAT5A" "ITGA2"  "CDH2"   "CTNNB1"
## [17] "CCND1" 
## 
## $Factor6of10
##  [1] "RB1"     "XIAP"    "ETS1"    "MAPK8"   "ARID1A"  "BID"     "CCND1"  
##  [8] "PIK3R1"  "CHEK1"   "IGF1R"   "SRSF1"   "TUBA1B"  "NRAS"    "MYH9"   
## [15] "CDKN1B"  "BCL2L11" "ERBB3"   "FOXO3"   "ACACA"   "NCOA3"   "GAB2"   
## [22] "MYC"     "EIF4G1"  "CDH2"    "EEF2"    "SQSTM1"  "G6PD"    "RBM15"  
## [29] "FASN"    "VHL"     "GAPDH"   "MSH6"   
## 
## $Factor7of10
##  [1] "ESR1"    "MET"     "BAP1"    "ERRFI1"  "G6PD"    "BCL2"    "KRAS"   
##  [8] "CCND1"   "NOTCH3"  "AKT1"    "IGF1R"   "PTEN"    "CDKN1B"  "IRS1"   
## [15] "MYC"     "JUN"     "BCL2L11" "EZH2"    "SHC1"    "XIAP"    "ETS1"   
## [22] "MAPK8"   "ARID1A"  "BID"     "YWHAZ"   "FOXO3"   "CHEK1"   "FN1"    
## [29] "NCOA3"   "AXL"     "PTK2"    "CDKN1A"  "EGFR"    "CAV1"    "CASP3"  
## [36] "ANXA1"   "TFF1"    "STAT3"   "ASNS"    "FOXM1"   "IGFBP2"  "ITGA2"  
## [43] "RET"     "SQSTM1"  "CCNE2"   "GAB2"    "NDRG1"   "INPP4B"  "LCN2"   
## [50] "RAD50"   "GATA3"   "CTNNB1" 
## 
## $Factor8of10
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "STAT5A" "CCND1"  "YAP1"   "MAPK1"  "ANLN"   "ITGA2"  "ERBB3"  "TGM2"  
## [25] "G6PD"  
## 
## $Factor9of10
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ETS1"  
## [17] "STAT5A" "CCND1"  "YAP1"   "MAPK1"  "ANLN"   "ITGA2"  "TGM2"   "G6PD"  
## [25] "FASN"  
## 
## $Factor10of10
##  [1] "RB1"    "XIAP"   "ETS1"   "MAPK8"  "ARID1A" "BID"    "MYH9"   "CDKN1A"
##  [9] "FOXO3"  "ATM"    "CASP8"  "MACC1"  "CCND1"  "PIK3R1" "CHEK1"  "IGF1R" 
## [17] "SRSF1"  "TUBA1B" "NRAS"   "NCOA3"  "GAB2"   "YAP1"   "MAPK1"  "ANLN"  
## [25] "IGFBP2" "FASN"   "CTNNB1" "TTF1"   "VHL"
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_fabia_top_5_percent.rds")

2. Pathway Analysis

A. GO Classification

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/24
## GO:0003824 GO:0003824           catalytic activity    16     16/24
## GO:0005198 GO:0005198 structural molecule activity     0      0/24
## GO:0005215 GO:0005215         transporter activity     0      0/24
## GO:0005488 GO:0005488                      binding    24     24/24
## GO:0009055 GO:0009055   electron transfer activity     0      0/24
##                                                                                                                                        geneID
## GO:0003774                                                                                                                               MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/MAPK1/TGM2/G6PD
## GO:0005198                                                                                                                                   
## GO:0005215                                                                                                                                   
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD
## GO:0009055                                                                                                                                   
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/24
## GO:0002376 GO:0002376 immune system process    14     14/24
## GO:0008152 GO:0008152     metabolic process    22     22/24
## GO:0009987 GO:0009987      cellular process    24     24/24
## GO:0016032 GO:0016032         viral process     3      3/24
## GO:0022414 GO:0022414  reproductive process     8      8/24
##                                                                                                                                        geneID
## GO:0000003                                                                                          AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                      HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/MAPK1/ITGA2/G6PD
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ITGA2/TGM2/G6PD
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD
## GO:0016032                                                                                                                  HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                          AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    14     14/24
## GO:0044423 GO:0044423           virion component     0      0/24
## GO:0110165 GO:0110165 cellular anatomical entity    24     24/24
##                                                                                                                                        geneID
## GO:0032991                                                     HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CCND1/YAP1/ITGA2/TGM2
## GO:0044423                                                                                                                                   
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/26
## GO:0003824 GO:0003824           catalytic activity    14     14/26
## GO:0005198 GO:0005198 structural molecule activity     1      1/26
## GO:0005215 GO:0005215         transporter activity     2      2/26
## GO:0005488 GO:0005488                      binding    26     26/26
## GO:0009055 GO:0009055   electron transfer activity     0      0/26
##                                                                                                                                                 geneID
## GO:0003774                                                                                                                                            
## GO:0003824                                                                    MET/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/MAPK8/PTEN/NRAS/PTK2/ATM/CHEK1/NCOA3
## GO:0005198                                                                                                                                         FN1
## GO:0005215                                                                                                                                  BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2/CTNNB1
## GO:0009055                                                                                                                                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     9      9/26
## GO:0002376 GO:0002376 immune system process    18     18/26
## GO:0008152 GO:0008152     metabolic process    24     24/26
## GO:0009987 GO:0009987      cellular process    26     26/26
## GO:0016032 GO:0016032         viral process     3      3/26
## GO:0022414 GO:0022414  reproductive process     9      9/26
##                                                                                                                                                 geneID
## GO:0000003                                                                                            ESR1/BCL2/AKT1/IGF1R/PTEN/ATM/FOXO3/ITGA2/CTNNB1
## GO:0002376                                             ESR1/G6PD/BCL2/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/FOXO3/FN1/GAB2/ITGA2/CTNNB1
## GO:0008152           ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/ITGA2/CTNNB1
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2/CTNNB1
## GO:0016032                                                                                                                             BCL2/AKT1/ITGA2
## GO:0022414                                                                                            ESR1/BCL2/AKT1/IGF1R/PTEN/ATM/FOXO3/ITGA2/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    16     16/26
## GO:0044423 GO:0044423           virion component     0      0/26
## GO:0110165 GO:0110165 cellular anatomical entity    26     26/26
##                                                                                                                                                 geneID
## GO:0032991                                                    ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/ETS1/ARID1A/ATM/FOXO3/CHEK1/FN1/NCOA3/ITGA2/CTNNB1
## GO:0044423                                                                                                                                            
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2/CTNNB1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/26
## GO:0003824 GO:0003824           catalytic activity    15     15/26
## GO:0005198 GO:0005198 structural molecule activity     1      1/26
## GO:0005215 GO:0005215         transporter activity     1      1/26
## GO:0005488 GO:0005488                      binding    26     26/26
## GO:0009055 GO:0009055   electron transfer activity     0      0/26
##                                                                                                                                                         geneID
## GO:0003774                                                                                                                                                MYH9
## GO:0003824                                                              XIAP/MAPK8/CDKN1A/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NCOA3/MAPK1/TGM2/G6PD/FASN
## GO:0005198                                                                                                                                              TUBA1B
## GO:0005215                                                                                                                                               IGF1R
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/G6PD/FASN
## GO:0009055                                                                                                                                                    
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     5      5/26
## GO:0002376 GO:0002376 immune system process    15     15/26
## GO:0008152 GO:0008152     metabolic process    23     23/26
## GO:0009987 GO:0009987      cellular process    26     26/26
## GO:0016032 GO:0016032         viral process     0      0/26
## GO:0022414 GO:0022414  reproductive process     5      5/26
##                                                                                                                                                         geneID
## GO:0000003                                                                                                                          MYH9/FOXO3/ATM/CASP8/IGF1R
## GO:0002376                                                                 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PIK3R1/IGF1R/GAB2/MAPK1/G6PD
## GO:0008152                  ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/MAPK1/TGM2/G6PD/FASN
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/G6PD/FASN
## GO:0016032                                                                                                                                                    
## GO:0022414                                                                                                                          MYH9/FOXO3/ATM/CASP8/IGF1R
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    16     16/26
## GO:0044423 GO:0044423           virion component     0      0/26
## GO:0110165 GO:0110165 cellular anatomical entity    26     26/26
##                                                                                                                                                         geneID
## GO:0032991                                                       ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/TGM2
## GO:0044423                                                                                                                                                    
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/G6PD/FASN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/25
## GO:0003824 GO:0003824           catalytic activity    16     16/25
## GO:0005198 GO:0005198 structural molecule activity     1      1/25
## GO:0005215 GO:0005215         transporter activity     2      2/25
## GO:0005488 GO:0005488                      binding    25     25/25
## GO:0009055 GO:0009055   electron transfer activity     0      0/25
##                                                                                                                                              geneID
## GO:0003774                                                                                                                                         
## GO:0003824                                                     MET/G6PD/KRAS/CCND1/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/PTEN/NRAS/PTK2/ATM/CDKN1A/CHEK1
## GO:0005198                                                                                                                                      FN1
## GO:0005215                                                                                                                               BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/PTEN/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/FOXO3/CHEK1/FN1/ITGA2/CTNNB1
## GO:0009055                                                                                                                                         
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    10     10/25
## GO:0002376 GO:0002376 immune system process    16     16/25
## GO:0008152 GO:0008152     metabolic process    24     24/25
## GO:0009987 GO:0009987      cellular process    25     25/25
## GO:0016032 GO:0016032         viral process     4      4/25
## GO:0022414 GO:0022414  reproductive process    10     10/25
##                                                                                                                                              geneID
## GO:0000003                                                                                    ESR1/BCL2/AKT1/IGF1R/MTOR/PTEN/ATM/FOXO3/ITGA2/CTNNB1
## GO:0002376                                                  ESR1/G6PD/BCL2/AKT1/IGF1R/HSPA1A/MTOR/MAPK8/PTK2/ETS1/ATM/CDKN1A/FOXO3/FN1/ITGA2/CTNNB1
## GO:0008152      ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/PTEN/PTK2/ETS1/ATM/CDKN1A/STAT5A/FOXO3/CHEK1/FN1/ITGA2/CTNNB1
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/PTEN/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/FOXO3/CHEK1/FN1/ITGA2/CTNNB1
## GO:0016032                                                                                                                   BCL2/AKT1/HSPA1A/ITGA2
## GO:0022414                                                                                    ESR1/BCL2/AKT1/IGF1R/MTOR/PTEN/ATM/FOXO3/ITGA2/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    18     18/25
## GO:0044423 GO:0044423           virion component     0      0/25
## GO:0110165 GO:0110165 cellular anatomical entity    25     25/25
##                                                                                                                                              geneID
## GO:0032991                                    ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/MTOR/ETS1/ATM/CDKN1A/STAT5A/FOXO3/CHEK1/FN1/ITGA2/CTNNB1
## GO:0044423                                                                                                                                         
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/PTEN/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/FOXO3/CHEK1/FN1/ITGA2/CTNNB1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/28
## GO:0003824 GO:0003824           catalytic activity    15     15/28
## GO:0005198 GO:0005198 structural molecule activity     1      1/28
## GO:0005215 GO:0005215         transporter activity     1      1/28
## GO:0005488 GO:0005488                      binding    28     28/28
## GO:0009055 GO:0009055   electron transfer activity     0      0/28
##                                                                                                                                                                     geneID
## GO:0003774                                                                                                                                                            MYH9
## GO:0003824                                                                          XIAP/MAPK8/CDKN1A/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NCOA3/MAPK1/TGM2/G6PD/FASN
## GO:0005198                                                                                                                                                          TUBA1B
## GO:0005215                                                                                                                                                           IGF1R
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/SQSTM1/G6PD/FASN/TTF1
## GO:0009055                                                                                                                                                                
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     5      5/28
## GO:0002376 GO:0002376 immune system process    16     16/28
## GO:0008152 GO:0008152     metabolic process    25     25/28
## GO:0009987 GO:0009987      cellular process    28     28/28
## GO:0016032 GO:0016032         viral process     0      0/28
## GO:0022414 GO:0022414  reproductive process     5      5/28
##                                                                                                                                                                     geneID
## GO:0000003                                                                                                                                      MYH9/FOXO3/ATM/CASP8/IGF1R
## GO:0002376                                                                      ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PIK3R1/IGF1R/GAB2/MAPK1/SQSTM1/G6PD
## GO:0008152                  ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/MAPK1/TGM2/SQSTM1/G6PD/FASN/TTF1
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/SQSTM1/G6PD/FASN/TTF1
## GO:0016032                                                                                                                                                                
## GO:0022414                                                                                                                                      MYH9/FOXO3/ATM/CASP8/IGF1R
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    16     16/28
## GO:0044423 GO:0044423           virion component     0      0/28
## GO:0110165 GO:0110165 cellular anatomical entity    28     28/28
##                                                                                                                                                                     geneID
## GO:0032991                                                                   ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/TGM2
## GO:0044423                                                                                                                                                                
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/SQSTM1/G6PD/FASN/TTF1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/52
## GO:0003824 GO:0003824           catalytic activity    22     22/52
## GO:0005198 GO:0005198 structural molecule activity     1      1/52
## GO:0005215 GO:0005215         transporter activity     2      2/52
## GO:0005488 GO:0005488                      binding    52     52/52
## GO:0009055 GO:0009055   electron transfer activity     0      0/52
##                                                                                                                                                                                                                                                                                                       geneID
## GO:0003774                                                                                                                                                                                                                                                                                                  
## GO:0003824                                                                                                                                                                             MET/BAP1/G6PD/KRAS/CCND1/AKT1/IGF1R/PTEN/EZH2/XIAP/MAPK8/CHEK1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CASP3/ASNS/RET/INPP4B/RAD50
## GO:0005198                                                                                                                                                                                                                                                                                               FN1
## GO:0005215                                                                                                                                                                                                                                                                                        BCL2/IGF1R
## GO:0005488 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/CTNNB1/GATA3
## GO:0009055                                                                                                                                                                                                                                                                                                  
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    19     19/52
## GO:0002376 GO:0002376 immune system process    33     33/52
## GO:0008152 GO:0008152     metabolic process    48     48/52
## GO:0009987 GO:0009987      cellular process    52     52/52
## GO:0016032 GO:0016032         viral process     7      7/52
## GO:0022414 GO:0022414  reproductive process    18     18/52
##                                                                                                                                                                                                                                                                                                       geneID
## GO:0000003                                                                                                                                                                                  ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/FOXO3/AXL/EGFR/CASP3/STAT3/IGFBP2/ITGA2/CCNE2/RAD50/CTNNB1/GATA3
## GO:0002376                                                                                                            ESR1/BAP1/G6PD/BCL2/AKT1/IGF1R/MYC/BCL2L11/EZH2/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/FN1/AXL/PTK2/CDKN1A/CAV1/CASP3/ANXA1/STAT3/IGFBP2/ITGA2/RET/SQSTM1/GAB2/NDRG1/LCN2/CTNNB1/GATA3
## GO:0008152                           ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/ITGA2/RET/SQSTM1/CCNE2/INPP4B/LCN2/RAD50/CTNNB1/GATA3
## GO:0009987 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/CTNNB1/GATA3
## GO:0016032                                                                                                                                                                                                                                                                 BCL2/AKT1/JUN/AXL/EGFR/CAV1/ITGA2
## GO:0022414                                                                                                                                                                                        ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/FOXO3/AXL/EGFR/CASP3/IGFBP2/ITGA2/CCNE2/RAD50/CTNNB1/GATA3
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    34     34/52
## GO:0044423 GO:0044423           virion component     0      0/52
## GO:0110165 GO:0110165 cellular anatomical entity    52     52/52
##                                                                                                                                                                                                                                                                                                       geneID
## GO:0032991                                                                                                      ESR1/MET/BAP1/BCL2/CCND1/NOTCH3/AKT1/IGF1R/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/ETS1/ARID1A/FOXO3/CHEK1/FN1/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/STAT3/FOXM1/ITGA2/RET/CCNE2/RAD50/CTNNB1/GATA3
## GO:0044423                                                                                                                                                                                                                                                                                                  
## GO:0110165 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/CTNNB1/GATA3
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/24
## GO:0003824 GO:0003824           catalytic activity    13     13/24
## GO:0005198 GO:0005198 structural molecule activity     1      1/24
## GO:0005215 GO:0005215         transporter activity     1      1/24
## GO:0005488 GO:0005488                      binding    24     24/24
## GO:0009055 GO:0009055   electron transfer activity     0      0/24
##                                                                                                                                               geneID
## GO:0003774                                                                                                                                      MYH9
## GO:0003824                                                              XIAP/MAPK8/CDKN1A/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NCOA3/MAPK1/FASN
## GO:0005198                                                                                                                                    TUBA1B
## GO:0005215                                                                                                                                     IGF1R
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/FASN
## GO:0009055                                                                                                                                          
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     5      5/24
## GO:0002376 GO:0002376 immune system process    14     14/24
## GO:0008152 GO:0008152     metabolic process    21     21/24
## GO:0009987 GO:0009987      cellular process    24     24/24
## GO:0016032 GO:0016032         viral process     0      0/24
## GO:0022414 GO:0022414  reproductive process     5      5/24
##                                                                                                                                               geneID
## GO:0000003                                                                                                                MYH9/FOXO3/ATM/CASP8/IGF1R
## GO:0002376                                                            ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PIK3R1/IGF1R/GAB2/MAPK1
## GO:0008152                  ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/MAPK1/FASN
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/FASN
## GO:0016032                                                                                                                                          
## GO:0022414                                                                                                                MYH9/FOXO3/ATM/CASP8/IGF1R
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    15     15/24
## GO:0044423 GO:0044423           virion component     0      0/24
## GO:0110165 GO:0110165 cellular anatomical entity    24     24/24
##                                                                                                                                               geneID
## GO:0032991                                                  ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1
## GO:0044423                                                                                                                                          
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/FASN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/25
## GO:0003824 GO:0003824           catalytic activity    17     17/25
## GO:0005198 GO:0005198 structural molecule activity     0      0/25
## GO:0005215 GO:0005215         transporter activity     0      0/25
## GO:0005488 GO:0005488                      binding    25     25/25
## GO:0009055 GO:0009055   electron transfer activity     0      0/25
##                                                                                                                                             geneID
## GO:0003774                                                                                                                                    MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/MAPK1/TGM2/G6PD/FASN
## GO:0005198                                                                                                                                        
## GO:0005215                                                                                                                                        
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD/FASN
## GO:0009055                                                                                                                                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/25
## GO:0002376 GO:0002376 immune system process    14     14/25
## GO:0008152 GO:0008152     metabolic process    23     23/25
## GO:0009987 GO:0009987      cellular process    25     25/25
## GO:0016032 GO:0016032         viral process     3      3/25
## GO:0022414 GO:0022414  reproductive process     8      8/25
##                                                                                                                                             geneID
## GO:0000003                                                                                               AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                           HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/MAPK1/ITGA2/G6PD
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ITGA2/TGM2/G6PD/FASN
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD/FASN
## GO:0016032                                                                                                                       HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                               AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    14     14/25
## GO:0044423 GO:0044423           virion component     0      0/25
## GO:0110165 GO:0110165 cellular anatomical entity    25     25/25
##                                                                                                                                             geneID
## GO:0032991                                                          HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CCND1/YAP1/ITGA2/TGM2
## GO:0044423                                                                                                                                        
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD/FASN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/28
## GO:0003824 GO:0003824           catalytic activity    15     15/28
## GO:0005198 GO:0005198 structural molecule activity     1      1/28
## GO:0005215 GO:0005215         transporter activity     2      2/28
## GO:0005488 GO:0005488                      binding    28     28/28
## GO:0009055 GO:0009055   electron transfer activity     0      0/28
##                                                                                                                                                              geneID
## GO:0003774                                                                                                                                                     MYH9
## GO:0003824                                                                          MET/G6PD/KRAS/CCND1/AKT1/IGF1R/CDKN1A/ATM/CASP8/PTEN/NRAS/PTK2/CHEK1/MAPK1/TGM2
## GO:0005198                                                                                                                                                      FN1
## GO:0005215                                                                                                                                               BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/STAT5A/CHEK1/FN1/YAP1/MAPK1/ANLN/ITGA2/CTNNB1/TGM2
## GO:0009055                                                                                                                                                         
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    11     11/28
## GO:0002376 GO:0002376 immune system process    16     16/28
## GO:0008152 GO:0008152     metabolic process    26     26/28
## GO:0009987 GO:0009987      cellular process    28     28/28
## GO:0016032 GO:0016032         viral process     3      3/28
## GO:0022414 GO:0022414  reproductive process    11     11/28
##                                                                                                                                                              geneID
## GO:0000003                                                                                              ESR1/BCL2/AKT1/IGF1R/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2/CTNNB1
## GO:0002376                                                                   ESR1/G6PD/BCL2/AKT1/IGF1R/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/FN1/MAPK1/ITGA2/CTNNB1
## GO:0008152           ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/PTK2/ETS1/STAT5A/CHEK1/FN1/YAP1/MAPK1/ITGA2/CTNNB1/TGM2
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/STAT5A/CHEK1/FN1/YAP1/MAPK1/ANLN/ITGA2/CTNNB1/TGM2
## GO:0016032                                                                                                                                          BCL2/AKT1/ITGA2
## GO:0022414                                                                                              ESR1/BCL2/AKT1/IGF1R/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    20     20/28
## GO:0044423 GO:0044423           virion component     0      0/28
## GO:0110165 GO:0110165 cellular anatomical entity    28     28/28
##                                                                                                                                                              geneID
## GO:0032991                                           ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CHEK1/FN1/YAP1/ITGA2/CTNNB1/TGM2
## GO:0044423                                                                                                                                                         
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/STAT5A/CHEK1/FN1/YAP1/MAPK1/ANLN/ITGA2/CTNNB1/TGM2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/53
## GO:0003824 GO:0003824           catalytic activity    24     24/53
## GO:0005198 GO:0005198 structural molecule activity     1      1/53
## GO:0005215 GO:0005215         transporter activity     2      2/53
## GO:0005488 GO:0005488                      binding    53     53/53
## GO:0009055 GO:0009055   electron transfer activity     0      0/53
##                                                                                                                                                                                                                                                                                                         geneID
## GO:0003774                                                                                                                                                                                                                                                                                                    
## GO:0003824                                                                                                                                                                      MET/BAP1/G6PD/KRAS/CCND1/AKT1/IGF1R/PTEN/EZH2/XIAP/MAPK8/NRAS/PTK2/ATM/CHEK1/NCOA3/AXL/CDKN1A/EGFR/CASP3/ASNS/RET/INPP4B/RAD50
## GO:0005198                                                                                                                                                                                                                                                                                                 FN1
## GO:0005215                                                                                                                                                                                                                                                                                          BCL2/IGF1R
## GO:0005488 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3
## GO:0009055                                                                                                                                                                                                                                                                                                    
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    19     19/53
## GO:0002376 GO:0002376 immune system process    33     33/53
## GO:0008152 GO:0008152     metabolic process    48     48/53
## GO:0009987 GO:0009987      cellular process    53     53/53
## GO:0016032 GO:0016032         viral process     7      7/53
## GO:0022414 GO:0022414  reproductive process    18     18/53
##                                                                                                                                                                                                                                                                                                         geneID
## GO:0000003                                                                                                                                                                                       ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/ATM/FOXO3/AXL/EGFR/CASP3/STAT3/IGFBP2/ITGA2/CCNE2/RAD50/GATA3
## GO:0002376                                                                                                                 ESR1/BAP1/G6PD/BCL2/AKT1/IGF1R/MYC/BCL2L11/EZH2/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/FOXO3/FN1/AXL/CDKN1A/CAV1/CASP3/ANXA1/STAT3/IGFBP2/ITGA2/RET/SQSTM1/GAB2/NDRG1/LCN2/GATA3
## GO:0008152                                ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/ITGA2/RET/SQSTM1/CCNE2/INPP4B/LCN2/RAD50/GATA3
## GO:0009987 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3
## GO:0016032                                                                                                                                                                                                                                                                   BCL2/AKT1/JUN/AXL/EGFR/CAV1/ITGA2
## GO:0022414                                                                                                                                                                                             ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/ATM/FOXO3/AXL/EGFR/CASP3/IGFBP2/ITGA2/CCNE2/RAD50/GATA3
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    34     34/53
## GO:0044423 GO:0044423           virion component     0      0/53
## GO:0110165 GO:0110165 cellular anatomical entity    53     53/53
##                                                                                                                                                                                                                                                                                                         geneID
## GO:0032991                                                                                                           ESR1/MET/BAP1/BCL2/CCND1/NOTCH3/AKT1/IGF1R/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/ETS1/ARID1A/ATM/FOXO3/CHEK1/FN1/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/STAT3/FOXM1/ITGA2/RET/CCNE2/RAD50/GATA3
## GO:0044423                                                                                                                                                                                                                                                                                                    
## GO:0110165 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/27
## GO:0003824 GO:0003824           catalytic activity    12     12/27
## GO:0005198 GO:0005198 structural molecule activity     1      1/27
## GO:0005215 GO:0005215         transporter activity     2      2/27
## GO:0005488 GO:0005488                      binding    27     27/27
## GO:0009055 GO:0009055   electron transfer activity     0      0/27
##                                                                                                                                                      geneID
## GO:0003774                                                                                                                                                 
## GO:0003824                                                                                   MET/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/MAPK8/CHEK1/NCOA3/FASN/VHL
## GO:0005198                                                                                                                                              FN1
## GO:0005215                                                                                                                                       BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/CDH2/GATA3/CTNNB1/RBM15/FASN/VHL
## GO:0009055                                                                                                                                                 
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/27
## GO:0002376 GO:0002376 immune system process    18     18/27
## GO:0008152 GO:0008152     metabolic process    25     25/27
## GO:0009987 GO:0009987      cellular process    27     27/27
## GO:0016032 GO:0016032         viral process     2      2/27
## GO:0022414 GO:0022414  reproductive process     8      8/27
##                                                                                                                                                      geneID
## GO:0000003                                                                                                      ESR1/BCL2/AKT1/IGF1R/RB1/FOXO3/GATA3/CTNNB1
## GO:0002376                                                 ESR1/G6PD/BCL2/AKT1/IGF1R/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/FN1/GAB2/GATA3/CTNNB1/RBM15
## GO:0008152           ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GATA3/CTNNB1/RBM15/FASN/VHL
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/CDH2/GATA3/CTNNB1/RBM15/FASN/VHL
## GO:0016032                                                                                                                                        BCL2/AKT1
## GO:0022414                                                                                                      ESR1/BCL2/AKT1/IGF1R/RB1/FOXO3/GATA3/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    18     18/27
## GO:0044423 GO:0044423           virion component     0      0/27
## GO:0110165 GO:0110165 cellular anatomical entity    27     27/27
##                                                                                                                                                      geneID
## GO:0032991                                              ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/RB1/ETS1/ARID1A/FOXO3/CHEK1/FN1/NCOA3/CDH2/GATA3/CTNNB1/RBM15
## GO:0044423                                                                                                                                                 
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/CDH2/GATA3/CTNNB1/RBM15/FASN/VHL
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/23
## GO:0003824 GO:0003824           catalytic activity    14     14/23
## GO:0005198 GO:0005198 structural molecule activity     1      1/23
## GO:0005215 GO:0005215         transporter activity     0      0/23
## GO:0005488 GO:0005488                      binding    23     23/23
## GO:0009055 GO:0009055   electron transfer activity     0      0/23
##                                                                                                                                  geneID
## GO:0003774                                                                                                                         MYH9
## GO:0003824                                                  HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/MAPK1
## GO:0005198                                                                                                                          FN1
## GO:0005215                                                                                                                             
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/FN1
## GO:0009055                                                                                                                             
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/23
## GO:0002376 GO:0002376 immune system process    14     14/23
## GO:0008152 GO:0008152     metabolic process    21     21/23
## GO:0009987 GO:0009987      cellular process    23     23/23
## GO:0016032 GO:0016032         viral process     3      3/23
## GO:0022414 GO:0022414  reproductive process     8      8/23
##                                                                                                                                  geneID
## GO:0000003                                                                                    AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/MAPK1/ITGA2/FN1
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ITGA2/FN1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/FN1
## GO:0016032                                                                                                            HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                    AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    14     14/23
## GO:0044423 GO:0044423           virion component     0      0/23
## GO:0110165 GO:0110165 cellular anatomical entity    23     23/23
##                                                                                                                                  geneID
## GO:0032991                                                HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CCND1/YAP1/ITGA2/FN1
## GO:0044423                                                                                                                             
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/FN1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/15
## GO:0003824 GO:0003824           catalytic activity    12     12/15
## GO:0005198 GO:0005198 structural molecule activity     0      0/15
## GO:0005215 GO:0005215         transporter activity     0      0/15
## GO:0005488 GO:0005488                      binding    15     15/15
## GO:0009055 GO:0009055   electron transfer activity     0      0/15
##                                                                                      geneID
## GO:0003774                                                                                 
## GO:0003824                   HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CDKN1A/G6PD
## GO:0005198                                                                                 
## GO:0005215                                                                                 
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/G6PD
## GO:0009055                                                                                 
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     5      5/15
## GO:0002376 GO:0002376 immune system process    10     10/15
## GO:0008152 GO:0008152     metabolic process    14     14/15
## GO:0009987 GO:0009987      cellular process    15     15/15
## GO:0016032 GO:0016032         viral process     3      3/15
## GO:0022414 GO:0022414  reproductive process     5      5/15
##                                                                                      geneID
## GO:0000003                                                         AKT1/MTOR/PTEN/ATM/ITGA2
## GO:0002376                           HSPA1A/AKT1/MTOR/MAPK8/PTK2/ETS1/ATM/CDKN1A/ITGA2/G6PD
## GO:0008152      HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/G6PD
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/G6PD
## GO:0016032                                                                HSPA1A/AKT1/ITGA2
## GO:0022414                                                         AKT1/MTOR/PTEN/ATM/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     8      8/15
## GO:0044423 GO:0044423           virion component     0      0/15
## GO:0110165 GO:0110165 cellular anatomical entity    15     15/15
##                                                                                      geneID
## GO:0032991                                    HSPA1A/AKT1/MTOR/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0044423                                                                                 
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/G6PD
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/11
## GO:0003824 GO:0003824           catalytic activity     6      6/11
## GO:0005198 GO:0005198 structural molecule activity     0      0/11
## GO:0005215 GO:0005215         transporter activity     0      0/11
## GO:0005488 GO:0005488                      binding    11     11/11
## GO:0009055 GO:0009055   electron transfer activity     0      0/11
##                                                                   geneID
## GO:0003774                                                              
## GO:0003824                             XIAP/MAPK8/CDKN1A/NCOA3/TGM2/FASN
## GO:0005198                                                              
## GO:0005215                                                              
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/CDKN1A/STAT5A/NCOA3/GAB2/TGM2/FASN
## GO:0009055                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0      0/11
## GO:0002376 GO:0002376 immune system process     7      7/11
## GO:0008152 GO:0008152     metabolic process    10     10/11
## GO:0009987 GO:0009987      cellular process    11     11/11
## GO:0016032 GO:0016032         viral process     0      0/11
## GO:0022414 GO:0022414  reproductive process     0      0/11
##                                                                   geneID
## GO:0000003                                                              
## GO:0002376                        ETS1/XIAP/MAPK8/ARID1A/BID/CDKN1A/GAB2
## GO:0008152      ETS1/XIAP/MAPK8/ARID1A/BID/CDKN1A/STAT5A/NCOA3/TGM2/FASN
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/CDKN1A/STAT5A/NCOA3/GAB2/TGM2/FASN
## GO:0016032                                                              
## GO:0022414                                                              
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     6      6/11
## GO:0044423 GO:0044423           virion component     0      0/11
## GO:0110165 GO:0110165 cellular anatomical entity    11     11/11
##                                                                   geneID
## GO:0032991                          ETS1/ARID1A/CDKN1A/STAT5A/NCOA3/TGM2
## GO:0044423                                                              
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/CDKN1A/STAT5A/NCOA3/GAB2/TGM2/FASN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/45
## GO:0003824 GO:0003824           catalytic activity    23     23/45
## GO:0005198 GO:0005198 structural molecule activity     0      0/45
## GO:0005215 GO:0005215         transporter activity     2      2/45
## GO:0005488 GO:0005488                      binding    45     45/45
## GO:0009055 GO:0009055   electron transfer activity     0      0/45
##                                                                                                                                                                                                                                                                 geneID
## GO:0003774                                                                                                                                                                                                                                                        MYH9
## GO:0003824                                                                                                                          XIAP/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/EZH2/RAB11B/NCOA3/CCND1/MAPK1/CASP3/MSH6/PIK3CA/MSH2/PRKAA1/G6PD
## GO:0005198                                                                                                                                                                                                                                                            
## GO:0005215                                                                                                                                                                                                                                                  IGF1R/BCL2
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/EZH2/RAB11B/NCOA3/GAB2/CCND1/YAP1/MAPK1/ANLN/ITGA2/BCL2/MYC/CASP3/BCL2L11/MSH6/PIK3CA/SRSF1/MSH2/CDH1/CTNNB1/IGFBP2/PRKAA1/YWHAB/G6PD/TFRC/PXN/NF2
## GO:0009055                                                                                                                                                                                                                                                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    17     17/45
## GO:0002376 GO:0002376 immune system process    28     28/45
## GO:0008152 GO:0008152     metabolic process    38     38/45
## GO:0009987 GO:0009987      cellular process    45     45/45
## GO:0016032 GO:0016032         viral process     3      3/45
## GO:0022414 GO:0022414  reproductive process    17     17/45
##                                                                                                                                                                                                                                                                 geneID
## GO:0000003                                                                                                                                                         MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/ITGA2/BCL2/CASP3/BCL2L11/MSH6/PIK3CA/MSH2/CTNNB1/IGFBP2
## GO:0002376                                                                                               ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PARP1/IGF1R/EZH2/GAB2/MAPK1/ITGA2/BCL2/MYC/CASP3/BCL2L11/MSH6/PIK3CA/MSH2/CTNNB1/IGFBP2/G6PD/TFRC
## GO:0008152                                         ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/PARP1/IGF1R/CCNE2/EZH2/RAB11B/NCOA3/CCND1/YAP1/MAPK1/ITGA2/BCL2/MYC/CASP3/MSH6/PIK3CA/SRSF1/MSH2/CDH1/CTNNB1/PRKAA1/YWHAB/G6PD/TFRC/NF2
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/EZH2/RAB11B/NCOA3/GAB2/CCND1/YAP1/MAPK1/ANLN/ITGA2/BCL2/MYC/CASP3/BCL2L11/MSH6/PIK3CA/SRSF1/MSH2/CDH1/CTNNB1/IGFBP2/PRKAA1/YWHAB/G6PD/TFRC/PXN/NF2
## GO:0016032                                                                                                                                                                                                                                             ITGA2/BCL2/TFRC
## GO:0022414                                                                                                                                                         MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/ITGA2/BCL2/CASP3/BCL2L11/MSH6/PIK3CA/MSH2/CTNNB1/IGFBP2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    28     28/45
## GO:0044423 GO:0044423           virion component     0      0/45
## GO:0110165 GO:0110165 cellular anatomical entity    45     45/45
##                                                                                                                                                                                                                                                                 geneID
## GO:0032991                                                                                             ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/PARP1/IGF1R/CCNE2/EZH2/NCOA3/CCND1/YAP1/ITGA2/BCL2/MYC/CASP3/BCL2L11/MSH6/PIK3CA/SRSF1/MSH2/CDH1/CTNNB1/PRKAA1/TFRC/PXN
## GO:0044423                                                                                                                                                                                                                                                            
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/EZH2/RAB11B/NCOA3/GAB2/CCND1/YAP1/MAPK1/ANLN/ITGA2/BCL2/MYC/CASP3/BCL2L11/MSH6/PIK3CA/SRSF1/MSH2/CDH1/CTNNB1/IGFBP2/PRKAA1/YWHAB/G6PD/TFRC/PXN/NF2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/17
## GO:0003824 GO:0003824           catalytic activity    12     12/17
## GO:0005198 GO:0005198 structural molecule activity     0      0/17
## GO:0005215 GO:0005215         transporter activity     0      0/17
## GO:0005488 GO:0005488                      binding    17     17/17
## GO:0009055 GO:0009055   electron transfer activity     0      0/17
##                                                                                                   geneID
## GO:0003774                                                                                              
## GO:0003824                               HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CDKN1A/CCND1
## GO:0005198                                                                                              
## GO:0005215                                                                                              
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/CDH2/CTNNB1/CCND1
## GO:0009055                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     6      6/17
## GO:0002376 GO:0002376 immune system process    10     10/17
## GO:0008152 GO:0008152     metabolic process    15     15/17
## GO:0009987 GO:0009987      cellular process    17     17/17
## GO:0016032 GO:0016032         viral process     3      3/17
## GO:0022414 GO:0022414  reproductive process     6      6/17
##                                                                                                   geneID
## GO:0000003                                                               AKT1/MTOR/PTEN/ATM/ITGA2/CTNNB1
## GO:0002376                                      HSPA1A/AKT1/MTOR/MAPK8/PTK2/ETS1/ATM/CDKN1A/ITGA2/CTNNB1
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/CTNNB1/CCND1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/CDH2/CTNNB1/CCND1
## GO:0016032                                                                             HSPA1A/AKT1/ITGA2
## GO:0022414                                                               AKT1/MTOR/PTEN/ATM/ITGA2/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    11     11/17
## GO:0044423 GO:0044423           virion component     0      0/17
## GO:0110165 GO:0110165 cellular anatomical entity    17     17/17
##                                                                                                   geneID
## GO:0032991                               HSPA1A/AKT1/MTOR/ETS1/ATM/CDKN1A/STAT5A/ITGA2/CDH2/CTNNB1/CCND1
## GO:0044423                                                                                              
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2/CDH2/CTNNB1/CCND1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/32
## GO:0003824 GO:0003824           catalytic activity    16     16/32
## GO:0005198 GO:0005198 structural molecule activity     1      1/32
## GO:0005215 GO:0005215         transporter activity     1      1/32
## GO:0005488 GO:0005488                      binding    32     32/32
## GO:0009055 GO:0009055   electron transfer activity     0      0/32
##                                                                                                                                                                                           geneID
## GO:0003774                                                                                                                                                                                  MYH9
## GO:0003824                                                                                             XIAP/MAPK8/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NRAS/ACACA/NCOA3/EEF2/G6PD/FASN/VHL/GAPDH/MSH6
## GO:0005198                                                                                                                                                                                TUBA1B
## GO:0005215                                                                                                                                                                                 IGF1R
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/MYH9/CDKN1B/BCL2L11/ERBB3/FOXO3/ACACA/NCOA3/GAB2/MYC/EIF4G1/CDH2/EEF2/SQSTM1/G6PD/RBM15/FASN/VHL/GAPDH/MSH6
## GO:0009055                                                                                                                                                                                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     7      7/32
## GO:0002376 GO:0002376 immune system process    18     18/32
## GO:0008152 GO:0008152     metabolic process    27     27/32
## GO:0009987 GO:0009987      cellular process    32     32/32
## GO:0016032 GO:0016032         viral process     0      0/32
## GO:0022414 GO:0022414  reproductive process     7      7/32
##                                                                                                                                                                                           geneID
## GO:0000003                                                                                                                                              RB1/IGF1R/MYH9/CDKN1B/BCL2L11/FOXO3/MSH6
## GO:0002376                                                                                  RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PIK3R1/IGF1R/MYH9/BCL2L11/FOXO3/GAB2/MYC/SQSTM1/G6PD/RBM15/GAPDH/MSH6
## GO:0008152                               RB1/XIAP/ETS1/MAPK8/ARID1A/BID/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/MYH9/CDKN1B/ERBB3/FOXO3/ACACA/NCOA3/MYC/EIF4G1/EEF2/SQSTM1/G6PD/RBM15/FASN/VHL/GAPDH/MSH6
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/MYH9/CDKN1B/BCL2L11/ERBB3/FOXO3/ACACA/NCOA3/GAB2/MYC/EIF4G1/CDH2/EEF2/SQSTM1/G6PD/RBM15/FASN/VHL/GAPDH/MSH6
## GO:0016032                                                                                                                                                                                      
## GO:0022414                                                                                                                                              RB1/IGF1R/MYH9/CDKN1B/BCL2L11/FOXO3/MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    21     21/32
## GO:0044423 GO:0044423           virion component     0      0/32
## GO:0110165 GO:0110165 cellular anatomical entity    32     32/32
##                                                                                                                                                                                           geneID
## GO:0032991                                                            RB1/ETS1/ARID1A/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/MYH9/CDKN1B/BCL2L11/ERBB3/FOXO3/NCOA3/MYC/EIF4G1/CDH2/EEF2/RBM15/GAPDH/MSH6
## GO:0044423                                                                                                                                                                                      
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/MYH9/CDKN1B/BCL2L11/ERBB3/FOXO3/ACACA/NCOA3/GAB2/MYC/EIF4G1/CDH2/EEF2/SQSTM1/G6PD/RBM15/FASN/VHL/GAPDH/MSH6
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/52
## GO:0003824 GO:0003824           catalytic activity    22     22/52
## GO:0005198 GO:0005198 structural molecule activity     1      1/52
## GO:0005215 GO:0005215         transporter activity     2      2/52
## GO:0005488 GO:0005488                      binding    52     52/52
## GO:0009055 GO:0009055   electron transfer activity     0      0/52
##                                                                                                                                                                                                                                                                                                       geneID
## GO:0003774                                                                                                                                                                                                                                                                                                  
## GO:0003824                                                                                                                                                                             MET/BAP1/G6PD/KRAS/CCND1/AKT1/IGF1R/PTEN/EZH2/XIAP/MAPK8/CHEK1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CASP3/ASNS/RET/INPP4B/RAD50
## GO:0005198                                                                                                                                                                                                                                                                                               FN1
## GO:0005215                                                                                                                                                                                                                                                                                        BCL2/IGF1R
## GO:0005488 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3/CTNNB1
## GO:0009055                                                                                                                                                                                                                                                                                                  
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    19     19/52
## GO:0002376 GO:0002376 immune system process    33     33/52
## GO:0008152 GO:0008152     metabolic process    48     48/52
## GO:0009987 GO:0009987      cellular process    52     52/52
## GO:0016032 GO:0016032         viral process     7      7/52
## GO:0022414 GO:0022414  reproductive process    18     18/52
##                                                                                                                                                                                                                                                                                                       geneID
## GO:0000003                                                                                                                                                                                  ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/FOXO3/AXL/EGFR/CASP3/STAT3/IGFBP2/ITGA2/CCNE2/RAD50/GATA3/CTNNB1
## GO:0002376                                                                                                            ESR1/BAP1/G6PD/BCL2/AKT1/IGF1R/MYC/BCL2L11/EZH2/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/FN1/AXL/PTK2/CDKN1A/CAV1/CASP3/ANXA1/STAT3/IGFBP2/ITGA2/RET/SQSTM1/GAB2/NDRG1/LCN2/GATA3/CTNNB1
## GO:0008152                           ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/ITGA2/RET/SQSTM1/CCNE2/INPP4B/LCN2/RAD50/GATA3/CTNNB1
## GO:0009987 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3/CTNNB1
## GO:0016032                                                                                                                                                                                                                                                                 BCL2/AKT1/JUN/AXL/EGFR/CAV1/ITGA2
## GO:0022414                                                                                                                                                                                        ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/FOXO3/AXL/EGFR/CASP3/IGFBP2/ITGA2/CCNE2/RAD50/GATA3/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    34     34/52
## GO:0044423 GO:0044423           virion component     0      0/52
## GO:0110165 GO:0110165 cellular anatomical entity    52     52/52
##                                                                                                                                                                                                                                                                                                       geneID
## GO:0032991                                                                                                      ESR1/MET/BAP1/BCL2/CCND1/NOTCH3/AKT1/IGF1R/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/ETS1/ARID1A/FOXO3/CHEK1/FN1/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/STAT3/FOXM1/ITGA2/RET/CCNE2/RAD50/GATA3/CTNNB1
## GO:0044423                                                                                                                                                                                                                                                                                                  
## GO:0110165 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/AXL/PTK2/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/STAT3/ASNS/FOXM1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3/CTNNB1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/25
## GO:0003824 GO:0003824           catalytic activity    16     16/25
## GO:0005198 GO:0005198 structural molecule activity     0      0/25
## GO:0005215 GO:0005215         transporter activity     0      0/25
## GO:0005488 GO:0005488                      binding    25     25/25
## GO:0009055 GO:0009055   electron transfer activity     0      0/25
##                                                                                                                                              geneID
## GO:0003774                                                                                                                                     MYH9
## GO:0003824                                                    HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/MAPK1/TGM2/G6PD
## GO:0005198                                                                                                                                         
## GO:0005215                                                                                                                                         
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/ERBB3/TGM2/G6PD
## GO:0009055                                                                                                                                         
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/25
## GO:0002376 GO:0002376 immune system process    14     14/25
## GO:0008152 GO:0008152     metabolic process    23     23/25
## GO:0009987 GO:0009987      cellular process    25     25/25
## GO:0016032 GO:0016032         viral process     3      3/25
## GO:0022414 GO:0022414  reproductive process     8      8/25
##                                                                                                                                              geneID
## GO:0000003                                                                                                AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                            HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/MAPK1/ITGA2/G6PD
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ITGA2/ERBB3/TGM2/G6PD
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/ERBB3/TGM2/G6PD
## GO:0016032                                                                                                                        HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                                AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    15     15/25
## GO:0044423 GO:0044423           virion component     0      0/25
## GO:0110165 GO:0110165 cellular anatomical entity    25     25/25
##                                                                                                                                              geneID
## GO:0032991                                                     HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CCND1/YAP1/ITGA2/ERBB3/TGM2
## GO:0044423                                                                                                                                         
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/ERBB3/TGM2/G6PD
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/25
## GO:0003824 GO:0003824           catalytic activity    17     17/25
## GO:0005198 GO:0005198 structural molecule activity     0      0/25
## GO:0005215 GO:0005215         transporter activity     0      0/25
## GO:0005488 GO:0005488                      binding    25     25/25
## GO:0009055 GO:0009055   electron transfer activity     0      0/25
##                                                                                                                                             geneID
## GO:0003774                                                                                                                                    MYH9
## GO:0003824                                              HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/MAPK1/TGM2/G6PD/FASN
## GO:0005198                                                                                                                                        
## GO:0005215                                                                                                                                        
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD/FASN
## GO:0009055                                                                                                                                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/25
## GO:0002376 GO:0002376 immune system process    14     14/25
## GO:0008152 GO:0008152     metabolic process    23     23/25
## GO:0009987 GO:0009987      cellular process    25     25/25
## GO:0016032 GO:0016032         viral process     3      3/25
## GO:0022414 GO:0022414  reproductive process     8      8/25
##                                                                                                                                             geneID
## GO:0000003                                                                                               AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376                                                           HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/MAPK1/ITGA2/G6PD
## GO:0008152           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ITGA2/TGM2/G6PD/FASN
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD/FASN
## GO:0016032                                                                                                                       HSPA1A/AKT1/ITGA2
## GO:0022414                                                                                               AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    14     14/25
## GO:0044423 GO:0044423           virion component     0      0/25
## GO:0110165 GO:0110165 cellular anatomical entity    25     25/25
##                                                                                                                                             geneID
## GO:0032991                                                          HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CCND1/YAP1/ITGA2/TGM2
## GO:0044423                                                                                                                                        
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/MAPK1/ANLN/ITGA2/TGM2/G6PD/FASN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/29
## GO:0003824 GO:0003824           catalytic activity    15     15/29
## GO:0005198 GO:0005198 structural molecule activity     1      1/29
## GO:0005215 GO:0005215         transporter activity     1      1/29
## GO:0005488 GO:0005488                      binding    29     29/29
## GO:0009055 GO:0009055   electron transfer activity     0      0/29
##                                                                                                                                                                        geneID
## GO:0003774                                                                                                                                                               MYH9
## GO:0003824                                                                              XIAP/MAPK8/CDKN1A/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NRAS/NCOA3/MAPK1/FASN/VHL
## GO:0005198                                                                                                                                                             TUBA1B
## GO:0005215                                                                                                                                                              IGF1R
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/NCOA3/GAB2/YAP1/MAPK1/ANLN/IGFBP2/FASN/CTNNB1/TTF1/VHL
## GO:0009055                                                                                                                                                                   
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     8      8/29
## GO:0002376 GO:0002376 immune system process    17     17/29
## GO:0008152 GO:0008152     metabolic process    24     24/29
## GO:0009987 GO:0009987      cellular process    29     29/29
## GO:0016032 GO:0016032         viral process     0      0/29
## GO:0022414 GO:0022414  reproductive process     8      8/29
##                                                                                                                                                                        geneID
## GO:0000003                                                                                                                       RB1/MYH9/FOXO3/ATM/CASP8/IGF1R/IGFBP2/CTNNB1
## GO:0002376                                                                   RB1/XIAP/ETS1/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PIK3R1/IGF1R/GAB2/MAPK1/IGFBP2/CTNNB1
## GO:0008152                              RB1/XIAP/ETS1/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/NCOA3/YAP1/MAPK1/FASN/CTNNB1/TTF1/VHL
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/NCOA3/GAB2/YAP1/MAPK1/ANLN/IGFBP2/FASN/CTNNB1/TTF1/VHL
## GO:0016032                                                                                                                                                                   
## GO:0022414                                                                                                                       RB1/MYH9/FOXO3/ATM/CASP8/IGF1R/IGFBP2/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    16     16/29
## GO:0044423 GO:0044423           virion component     0      0/29
## GO:0110165 GO:0110165 cellular anatomical entity    29     29/29
##                                                                                                                                                                        geneID
## GO:0032991                                                                       RB1/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/NCOA3/YAP1/CTNNB1
## GO:0044423                                                                                                                                                                   
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/NCOA3/GAB2/YAP1/MAPK1/ANLN/IGFBP2/FASN/CTNNB1/TTF1/VHL
barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, Bicluster 1 of 1")

barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, Bicluster 1 of 2")

barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, Bicluster 2 of 2")

barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, Bicluster 1 of 3")

barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, Bicluster 2 of 3")

barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, Bicluster 3 of 3")

barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, Bicluster 1 of 5")

barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, Bicluster 2 of 5")

barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, Bicluster 3 of 5")

barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, Bicluster 4 of 5")

barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, Bicluster 5 of 5")

barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, Bicluster 1 of 10")

barplot(ggo_MF[[13]], title = "groupGO, Molecular Function, Bicluster 2 of 10")

barplot(ggo_MF[[14]], title = "groupGO, Molecular Function, Bicluster 3 of 10")

barplot(ggo_MF[[15]], title = "groupGO, Molecular Function, Bicluster 4 of 10")

barplot(ggo_MF[[16]], title = "groupGO, Molecular Function, Bicluster 5 of 10")

barplot(ggo_MF[[17]], title = "groupGO, Molecular Function, Bicluster 6 of 10")

barplot(ggo_MF[[18]], title = "groupGO, Molecular Function, Bicluster 7 of 10")

barplot(ggo_MF[[19]], title = "groupGO, Molecular Function, Bicluster 8 of 10")

barplot(ggo_MF[[20]], title = "groupGO, Molecular Function, Bicluster 9 of 10")

barplot(ggo_MF[[21]], title = "groupGO, Molecular Function, Bicluster 10 of 10")

barplot(ggo_BP[[1]], title = "groupGO, Biological Process, Bicluster 1 of 1")

barplot(ggo_BP[[2]], title = "groupGO, Biological Process, Bicluster 1 of 2")

barplot(ggo_BP[[3]], title = "groupGO, Biological Process, Bicluster 2 of 2")

barplot(ggo_BP[[4]], title = "groupGO, Biological Process, Bicluster 1 of 3")

barplot(ggo_BP[[5]], title = "groupGO, Biological Process, Bicluster 2 of 3")

barplot(ggo_BP[[6]], title = "groupGO, Biological Process, Bicluster 3 of 3")

barplot(ggo_BP[[7]], title = "groupGO, Biological Process, Bicluster 1 of 5")

barplot(ggo_BP[[8]], title = "groupGO, Biological Process, Bicluster 2 of 5")

barplot(ggo_BP[[9]], title = "groupGO, Biological Process, Bicluster 3 of 5")

barplot(ggo_BP[[10]], title = "groupGO, Biological Process, Bicluster 4 of 5")

barplot(ggo_BP[[11]], title = "groupGO, Biological Process, Bicluster 5 of 5")

barplot(ggo_BP[[12]], title = "groupGO, Biological Process, Bicluster 1 of 10")

barplot(ggo_BP[[13]], title = "groupGO, Biological Process, Bicluster 2 of 10")

barplot(ggo_BP[[14]], title = "groupGO, Biological Process, Bicluster 3 of 10")

barplot(ggo_BP[[15]], title = "groupGO, Biological Process, Bicluster 4 of 10")

barplot(ggo_BP[[16]], title = "groupGO, Biological Process, Bicluster 5 of 10")

barplot(ggo_BP[[17]], title = "groupGO, Biological Process, Bicluster 6 of 10")

barplot(ggo_BP[[18]], title = "groupGO, Biological Process, Bicluster 7 of 10")

barplot(ggo_BP[[19]], title = "groupGO, Biological Process, Bicluster 8 of 10")

barplot(ggo_BP[[20]], title = "groupGO, Biological Process, Bicluster 9 of 10")

barplot(ggo_BP[[21]], title = "groupGO, Biological Process, Bicluster 10 of 10")

barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, Bicluster 1 of 1")

barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, Bicluster 1 of 2")

barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, Bicluster 2 of 2")

barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, Bicluster 1 of 3")

barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, Bicluster 2 of 3")

barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, Bicluster 3 of 3")

barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, Bicluster 1 of 5")

barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, Bicluster 2 of 5")

barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, Bicluster 3 of 5")

barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, Bicluster 4 of 5")

barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, Bicluster 5 of 5")

barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, Bicluster 1 of 10")

barplot(ggo_CC[[13]], title = "groupGO, Cellular Component, Bicluster 2 of 10")

barplot(ggo_CC[[14]], title = "groupGO, Cellular Component, Bicluster 3 of 10")

barplot(ggo_CC[[15]], title = "groupGO, Cellular Component, Bicluster 4 of 10")

barplot(ggo_CC[[16]], title = "groupGO, Cellular Component, Bicluster 5 of 10")

barplot(ggo_CC[[17]], title = "groupGO, Cellular Component, Bicluster 6 of 10")

barplot(ggo_CC[[18]], title = "groupGO, Cellular Component, Bicluster 7 of 10")

barplot(ggo_CC[[19]], title = "groupGO, Cellular Component, Bicluster 8 of 10")

barplot(ggo_CC[[20]], title = "groupGO, Cellular Component, Bicluster 9 of 10")

barplot(ggo_CC[[21]], title = "groupGO, Cellular Component, Bicluster 10 of 10")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21
for(z in 1:length(geneNames)){
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID                                        Description
## GO:0106310 GO:0106310                     protein serine kinase activity
## GO:0004674 GO:0004674           protein serine/threonine kinase activity
## GO:0004707 GO:0004707                                MAP kinase activity
## GO:0070064 GO:0070064                        proline-rich region binding
## GO:0042826 GO:0042826                        histone deacetylase binding
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0106310      5/24 363/18522 0.0000879512 0.009839616 0.004097469
## GO:0004674      5/24 427/18522 0.0001882293 0.009839616 0.004097469
## GO:0004707      2/24  16/18522 0.0001909646 0.009839616 0.004097469
## GO:0070064      2/24  17/18522 0.0002162553 0.009839616 0.004097469
## GO:0042826      3/24 128/18522 0.0005867501 0.021357704 0.008893896
## GO:0030291      2/24  37/18522 0.0010423909 0.024142433 0.010053529
##                               geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
## GO:0030291               AKT1/CDKN1A     2
##                    ID                                 Description GeneRatio
## GO:0010631 GO:0010631                   epithelial cell migration      9/24
## GO:0090132 GO:0090132                        epithelium migration      9/24
## GO:0090130 GO:0090130                            tissue migration      9/24
## GO:0062197 GO:0062197        cellular response to chemical stress      8/24
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/24
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/24
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010631 375/18888 4.378338e-10 3.493448e-07 1.434282e-07
## GO:0090132 378/18888 4.697252e-10 3.493448e-07 1.434282e-07
## GO:0090130 383/18888 5.274456e-10 3.493448e-07 1.434282e-07
## GO:0062197 311/18888 2.888334e-09 1.434780e-06 5.890681e-07
## GO:0071214 334/18888 5.054206e-09 1.495343e-06 6.139332e-07
## GO:0104004 334/18888 5.054206e-09 1.495343e-06 6.139332e-07
##                                                     geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0062197     HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1/G6PD     8
## GO:0071214     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                         Description GeneRatio   BgRatio
## GO:0005925 GO:0005925                      focal adhesion      7/24 421/19894
## GO:0030055 GO:0030055             cell-substrate junction      7/24 431/19894
## GO:0005826 GO:0005826         actomyosin contractile ring      2/24   4/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane      4/24 161/19894
## GO:0070938 GO:0070938                    contractile ring      2/24  10/19894
## GO:0098562 GO:0098562        cytoplasmic side of membrane      4/24 199/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 4.585265e-07 3.409715e-05 1.921762e-05
## GO:0030055 5.369630e-07 3.409715e-05 1.921762e-05
## GO:0005826 8.356555e-06 3.537608e-04 1.993845e-04
## GO:0009898 3.869971e-05 1.228716e-03 6.925211e-04
## GO:0070938 6.239748e-05 1.584896e-03 8.932692e-04
## GO:0098562 8.823680e-05 1.867679e-03 1.052650e-03
##                                            geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0005826                              MYH9/ANLN     2
## GO:0009898                    MYH9/PTEN/KRAS/G6PD     4
## GO:0070938                              MYH9/ANLN     2
## GO:0098562                    MYH9/PTEN/KRAS/G6PD     4
##                    ID                              Description GeneRatio
## GO:0019903 GO:0019903              protein phosphatase binding      5/26
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      7/26
## GO:0019902 GO:0019902                      phosphatase binding      5/26
## GO:0001221 GO:0001221        transcription coregulator binding      4/26
## GO:0016922 GO:0016922                 nuclear receptor binding      4/26
## GO:0001222 GO:0001222        transcription corepressor binding      3/26
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0019903 142/18522 1.425899e-06 0.0002965870 0.0001380871
## GO:0140297 478/18522 3.136151e-06 0.0003261597 0.0001518557
## GO:0019902 189/18522 5.798930e-06 0.0004020591 0.0001871935
## GO:0001221 114/18522 1.832807e-05 0.0009530599 0.0004437323
## GO:0016922 136/18522 3.667174e-05 0.0010300946 0.0004795987
## GO:0001222  47/18522 3.821623e-05 0.0010300946 0.0004795987
##                                              geneID Count
## GO:0019903               MET/BCL2/MAPK8/PTK2/CTNNB1     5
## GO:0140297 ESR1/BCL2/ETS1/ARID1A/YWHAZ/NCOA3/CTNNB1     7
## GO:0019902               MET/BCL2/MAPK8/PTK2/CTNNB1     5
## GO:0001221                   ESR1/ETS1/FOXO3/CTNNB1     4
## GO:0016922                 ESR1/ARID1A/NCOA3/CTNNB1     4
## GO:0001222                         ESR1/ETS1/CTNNB1     3
##                    ID                                         Description
## GO:0051402 GO:0051402                            neuron apoptotic process
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806      regulation of cell cycle G1/S phase transition
## GO:1901990 GO:1901990   regulation of mitotic cell cycle phase transition
## GO:0000082 GO:0000082               G1/S transition of mitotic cell cycle
## GO:0043523 GO:0043523              regulation of neuron apoptotic process
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051402      9/26 292/18888 1.106898e-10 2.477237e-07 9.798956e-08
## GO:2000045      7/26 185/18888 4.338048e-09 4.854276e-06 1.920157e-06
## GO:1902806      7/26 211/18888 1.079622e-08 8.053980e-06 3.185832e-06
## GO:1901990      8/26 356/18888 1.710620e-08 9.570921e-06 3.785873e-06
## GO:0000082      7/26 234/18888 2.204334e-08 9.866597e-06 3.902831e-06
## GO:0043523      7/26 244/18888 2.939457e-08 1.096418e-05 4.336988e-06
##                                                    geneID Count
## GO:0051402 G6PD/BCL2/KRAS/CCND1/XIAP/BID/ATM/FOXO3/CTNNB1     9
## GO:2000045            BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM     7
## GO:1902806            BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM     7
## GO:1901990      BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM/CHEK1     8
## GO:0000082            BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM     7
## GO:0043523          G6PD/BCL2/KRAS/CCND1/ATM/FOXO3/CTNNB1     7
##                    ID                                       Description
## GO:0017053 GO:0017053                   transcription repressor complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0005741 GO:0005741                      mitochondrial outer membrane
## GO:0005925 GO:0005925                                    focal adhesion
## GO:0030055 GO:0030055                           cell-substrate junction
## GO:0031968 GO:0031968                          organelle outer membrane
##            GeneRatio   BgRatio       pvalue    p.adjust    qvalue
## GO:0017053      3/26  77/19894 0.0001359483 0.005897502 0.0033461
## GO:0090571      2/26  15/19894 0.0001706628 0.005897502 0.0033461
## GO:0005741      4/26 219/19894 0.0001766044 0.005897502 0.0033461
## GO:0005925      5/26 421/19894 0.0001888698 0.005897502 0.0033461
## GO:0030055      5/26 431/19894 0.0002106347 0.005897502 0.0033461
## GO:0031968      4/26 248/19894 0.0002839739 0.005897502 0.0033461
##                                  geneID Count
## GO:0017053           CCND1/FOXO3/CTNNB1     3
## GO:0090571                 FOXO3/CTNNB1     2
## GO:0005741          BCL2/KRAS/BID/FOXO3     4
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2/CTNNB1     5
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2/CTNNB1     5
## GO:0031968          BCL2/KRAS/BID/FOXO3     4
##                    ID
## GO:0043559 GO:0043559
## GO:0120283 GO:0120283
## GO:0043560 GO:0043560
## GO:0140993 GO:0140993
## GO:0004707 GO:0004707
## GO:0005068 GO:0005068
##                                                                Description
## GO:0043559                                                 insulin binding
## GO:0120283                         protein serine/threonine kinase binding
## GO:0043560                              insulin receptor substrate binding
## GO:0140993                                      histone modifying activity
## GO:0004707                                             MAP kinase activity
## GO:0005068 transmembrane receptor protein tyrosine kinase adaptor activity
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0043559      2/26   5/18522 1.889884e-05 0.003458487 0.001511907
## GO:0120283      2/26   7/18522 3.961902e-05 0.003625141 0.001584761
## GO:0043560      2/26  13/18522 1.463956e-04 0.006650055 0.002907128
## GO:0140993      4/26 207/18522 1.868027e-04 0.006650055 0.002907128
## GO:0004707      2/26  16/18522 2.246413e-04 0.006650055 0.002907128
## GO:0005068      2/26  17/18522 2.543737e-04 0.006650055 0.002907128
##                          geneID Count
## GO:0043559         PIK3R1/IGF1R     2
## GO:0120283           XIAP/MAPK8     2
## GO:0043560         PIK3R1/IGF1R     2
## GO:0140993 ATM/CHEK1/NCOA3/TGM2     4
## GO:0004707          MAPK8/MAPK1     2
## GO:0005068          PIK3R1/GAB2     2
##                    ID                                   Description GeneRatio
## GO:0030099 GO:0030099                  myeloid cell differentiation      9/26
## GO:0071214 GO:0071214         cellular response to abiotic stimulus      8/26
## GO:0104004 GO:0104004   cellular response to environmental stimulus      8/26
## GO:0051402 GO:0051402                      neuron apoptotic process      7/26
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      6/26
## GO:0071496 GO:0071496        cellular response to external stimulus      7/26
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0030099 439/18888 4.013892e-09 5.458224e-06 2.662727e-06
## GO:0071214 334/18888 1.040984e-08 5.458224e-06 2.662727e-06
## GO:0104004 334/18888 1.040984e-08 5.458224e-06 2.662727e-06
## GO:0051402 292/18888 1.004486e-07 3.950139e-05 1.927026e-05
## GO:0042770 188/18888 1.751351e-07 5.509752e-05 2.687864e-05
## GO:0071496 335/18888 2.552859e-07 6.692746e-05 3.264973e-05
##                                                        geneID Count
## GO:0030099 ETS1/MYH9/FOXO3/CASP8/PIK3R1/STAT5A/GAB2/G6PD/FASN     9
## GO:0071214     MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:0104004     MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:0051402                XIAP/BID/FOXO3/ATM/CASP8/CCND1/G6PD     7
## GO:0042770                   BID/CDKN1A/FOXO3/ATM/CCND1/CHEK1     6
## GO:0071496         MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/IGF1R/MAPK1     7
##                    ID
## GO:0005826 GO:0005826
## GO:0070938 GO:0070938
## GO:0061695 GO:0061695
## GO:1902911 GO:1902911
## GO:0000307 GO:0000307
## GO:0070557 GO:0070557
##                                                               Description
## GO:0005826                                    actomyosin contractile ring
## GO:0070938                                               contractile ring
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:1902911                                         protein kinase complex
## GO:0000307             cyclin-dependent protein kinase holoenzyme complex
## GO:0070557                                               PCNA-p21 complex
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0005826      2/26   4/19894 9.838827e-06 0.001180659 0.0006524696
## GO:0070938      2/26  10/19894 7.343589e-05 0.004406154 0.0024349797
## GO:0061695      4/26 308/19894 6.436502e-04 0.025746006 0.0142280561
## GO:1902911      3/26 150/19894 9.618296e-04 0.028854888 0.0159461221
## GO:0000307      2/26  56/19894 2.421991e-03 0.032954906 0.0182119217
## GO:0070557      1/26   2/19894 2.612211e-03 0.032954906 0.0182119217
##                               geneID Count
## GO:0005826                 MYH9/ANLN     2
## GO:0070938                 MYH9/ANLN     2
## GO:0061695 CDKN1A/CCND1/PIK3R1/IGF1R     4
## GO:1902911        CDKN1A/CCND1/IGF1R     3
## GO:0000307              CDKN1A/CCND1     2
## GO:0070557                    CDKN1A     1
##                    ID                              Description GeneRatio
## GO:0019903 GO:0019903              protein phosphatase binding      5/25
## GO:0019902 GO:0019902                      phosphatase binding      5/25
## GO:0001221 GO:0001221        transcription coregulator binding      4/25
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      6/25
## GO:0001222 GO:0001222        transcription corepressor binding      3/25
## GO:0030235 GO:0030235 nitric-oxide synthase regulator activity      2/25
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0019903 142/18522 1.158813e-06 0.0002398744 9.026546e-05
## GO:0019902 189/18522 4.722704e-06 0.0004887999 1.839369e-04
## GO:0001221 114/18522 1.558218e-05 0.0010751701 4.045898e-04
## GO:0140297 478/18522 3.340010e-05 0.0012619408 4.748722e-04
## GO:0001222  47/18522 3.386691e-05 0.0012619408 4.748722e-04
## GO:0030235   7/18522 3.657799e-05 0.0012619408 4.748722e-04
##                                      geneID Count
## GO:0019903       MET/BCL2/MAPK8/PTK2/CTNNB1     5
## GO:0019902       MET/BCL2/MAPK8/PTK2/CTNNB1     5
## GO:0001221           ESR1/ETS1/FOXO3/CTNNB1     4
## GO:0140297 ESR1/BCL2/VHL/ETS1/STAT5A/CTNNB1     6
## GO:0001222                 ESR1/ETS1/CTNNB1     3
## GO:0030235                        ESR1/AKT1     2
##                    ID                                      Description
## GO:0048660 GO:0048660   regulation of smooth muscle cell proliferation
## GO:0010634 GO:0010634 positive regulation of epithelial cell migration
## GO:0072331 GO:0072331        signal transduction by p53 class mediator
## GO:0048659 GO:0048659                 smooth muscle cell proliferation
## GO:0010632 GO:0010632          regulation of epithelial cell migration
## GO:0048732 GO:0048732                                gland development
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0048660      7/25 174/18888 2.085090e-09 1.292825e-06 4.589639e-07
## GO:0010634      7/25 177/18888 2.349149e-09 1.292825e-06 4.589639e-07
## GO:0072331      7/25 177/18888 2.349149e-09 1.292825e-06 4.589639e-07
## GO:0048659      7/25 178/18888 2.443261e-09 1.292825e-06 4.589639e-07
## GO:0010632      8/25 298/18888 2.994994e-09 1.292825e-06 4.589639e-07
## GO:0048732      9/25 449/18888 3.261963e-09 1.292825e-06 4.589639e-07
##                                                      geneID Count
## GO:0048660       NOTCH3/AKT1/IGF1R/PTEN/CDKN1A/ITGA2/CTNNB1     7
## GO:0010634             MET/AKT1/MTOR/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0072331            BCL2/AKT1/MTOR/ATM/CDKN1A/FOXO3/CHEK1     7
## GO:0048659       NOTCH3/AKT1/IGF1R/PTEN/CDKN1A/ITGA2/CTNNB1     7
## GO:0010632        MET/AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     8
## GO:0048732 ESR1/MET/BCL2/CCND1/AKT1/ATM/STAT5A/ITGA2/CTNNB1     9
##                    ID                                       Description
## GO:0017053 GO:0017053                   transcription repressor complex
## GO:0005741 GO:0005741                      mitochondrial outer membrane
## GO:0005925 GO:0005925                                    focal adhesion
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0030055 GO:0030055                           cell-substrate junction
## GO:0031968 GO:0031968                          organelle outer membrane
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0017053      3/25  77/19894 0.0001205973 0.005126383 0.002807479
## GO:0005741      4/25 219/19894 0.0001507289 0.005126383 0.002807479
## GO:0005925      5/25 421/19894 0.0001552282 0.005126383 0.002807479
## GO:0090571      2/25  15/19894 0.0001576036 0.005126383 0.002807479
## GO:0030055      5/25 431/19894 0.0001731886 0.005126383 0.002807479
## GO:0031968      4/25 248/19894 0.0002426479 0.005289851 0.002897003
##                                   geneID Count
## GO:0017053            CCND1/FOXO3/CTNNB1     3
## GO:0005741          BCL2/KRAS/MTOR/FOXO3     4
## GO:0005925 KRAS/HSPA1A/PTK2/ITGA2/CTNNB1     5
## GO:0090571                  FOXO3/CTNNB1     2
## GO:0030055 KRAS/HSPA1A/PTK2/ITGA2/CTNNB1     5
## GO:0031968          BCL2/KRAS/MTOR/FOXO3     4
##                    ID                             Description GeneRatio
## GO:0043559 GO:0043559                         insulin binding      2/28
## GO:0120283 GO:0120283 protein serine/threonine kinase binding      2/28
## GO:0031625 GO:0031625        ubiquitin protein ligase binding      5/28
## GO:0044389 GO:0044389   ubiquitin-like protein ligase binding      5/28
## GO:0043560 GO:0043560      insulin receptor substrate binding      2/28
## GO:0030971 GO:0030971        receptor tyrosine kinase binding      3/28
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0043559   5/18522 2.197605e-05 0.004285329 0.001966278
## GO:0120283   7/18522 4.606338e-05 0.004491180 0.002060730
## GO:0031625 305/18522 8.437280e-05 0.005465883 0.002507962
## GO:0044389 324/18522 1.121207e-04 0.005465883 0.002507962
## GO:0043560  13/18522 1.701346e-04 0.005762971 0.002644278
## GO:0030971  81/18522 2.439332e-04 0.005762971 0.002644278
##                                    geneID Count
## GO:0043559                   PIK3R1/IGF1R     2
## GO:0120283                     XIAP/MAPK8     2
## GO:0031625 BID/CDKN1A/CASP8/TUBA1B/SQSTM1     5
## GO:0044389 BID/CDKN1A/CASP8/TUBA1B/SQSTM1     5
## GO:0043560                   PIK3R1/IGF1R     2
## GO:0030971             PIK3R1/GAB2/SQSTM1     3
##                    ID                                   Description GeneRatio
## GO:0030099 GO:0030099                  myeloid cell differentiation      9/28
## GO:0071214 GO:0071214         cellular response to abiotic stimulus      8/28
## GO:0104004 GO:0104004   cellular response to environmental stimulus      8/28
## GO:0051402 GO:0051402                      neuron apoptotic process      7/28
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      6/28
## GO:0071496 GO:0071496        cellular response to external stimulus      7/28
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0030099 439/18888 8.513830e-09 1.072325e-05 5.333796e-06
## GO:0071214 334/18888 2.008100e-08 1.072325e-05 5.333796e-06
## GO:0104004 334/18888 2.008100e-08 1.072325e-05 5.333796e-06
## GO:0051402 292/18888 1.760785e-07 7.051944e-05 3.507669e-05
## GO:0042770 188/18888 2.818815e-07 9.031482e-05 4.492300e-05
## GO:0071496 335/18888 4.457061e-07 1.190035e-04 5.919289e-05
##                                                        geneID Count
## GO:0030099 ETS1/MYH9/FOXO3/CASP8/PIK3R1/STAT5A/GAB2/G6PD/FASN     9
## GO:0071214     MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:0104004     MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:0051402                XIAP/BID/FOXO3/ATM/CASP8/CCND1/G6PD     7
## GO:0042770                   BID/CDKN1A/FOXO3/ATM/CCND1/CHEK1     6
## GO:0071496         MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/IGF1R/MAPK1     7
##                    ID
## GO:0005826 GO:0005826
## GO:0070938 GO:0070938
## GO:0061695 GO:0061695
## GO:1902911 GO:1902911
## GO:0000307 GO:0000307
## GO:0070557 GO:0070557
##                                                               Description
## GO:0005826                                    actomyosin contractile ring
## GO:0070938                                               contractile ring
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:1902911                                         protein kinase complex
## GO:0000307             cyclin-dependent protein kinase holoenzyme complex
## GO:0070557                                               PCNA-p21 complex
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0005826      2/28   4/19894 1.144178e-05 0.001601849 0.0009394301
## GO:0070938      2/28  10/19894 8.536580e-05 0.005975606 0.0035044906
## GO:0061695      4/28 308/19894 8.603303e-04 0.040148747 0.0235458816
## GO:1902911      3/28 150/19894 1.198614e-03 0.041951489 0.0246031289
## GO:0000307      2/28  56/19894 2.806822e-03 0.043605516 0.0255731596
## GO:0070557      1/28   2/19894 2.813009e-03 0.043605516 0.0255731596
##                               geneID Count
## GO:0005826                 MYH9/ANLN     2
## GO:0070938                 MYH9/ANLN     2
## GO:0061695 CDKN1A/CCND1/PIK3R1/IGF1R     4
## GO:1902911        CDKN1A/CCND1/IGF1R     3
## GO:0000307              CDKN1A/CCND1     2
## GO:0070557                    CDKN1A     1
##                    ID                              Description GeneRatio
## GO:0140313 GO:0140313          molecular sequestering activity      6/52
## GO:0019903 GO:0019903              protein phosphatase binding      8/52
## GO:0001221 GO:0001221        transcription coregulator binding      7/52
## GO:0019902 GO:0019902                      phosphatase binding      8/52
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     11/52
## GO:0031625 GO:0031625         ubiquitin protein ligase binding      9/52
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140313  49/18522 4.635728e-09 9.335950e-07 4.228370e-07
## GO:0019903 142/18522 5.540623e-09 9.335950e-07 4.228370e-07
## GO:0001221 114/18522 2.956987e-08 3.321682e-06 1.504432e-06
## GO:0019902 189/18522 5.195320e-08 4.377057e-06 1.982425e-06
## GO:0140297 478/18522 7.007675e-08 4.723173e-06 2.139185e-06
## GO:0031625 305/18522 1.564085e-07 8.784942e-06 3.978812e-06
##                                                                  geneID Count
## GO:0140313                          YWHAZ/CDKN1A/CAV1/STAT3/SQSTM1/LCN2     6
## GO:0019903                 MET/BCL2/CDKN1B/MAPK8/PTK2/EGFR/STAT3/CTNNB1     8
## GO:0001221                        ESR1/MYC/EZH2/ETS1/FOXO3/CTNNB1/GATA3     7
## GO:0019902                 MET/BCL2/CDKN1B/MAPK8/PTK2/EGFR/STAT3/CTNNB1     8
## GO:0140297 ESR1/BCL2/MYC/JUN/ETS1/ARID1A/YWHAZ/NCOA3/STAT3/CTNNB1/GATA3    11
## GO:0031625          BCL2/CDKN1B/JUN/BID/YWHAZ/CDKN1A/EGFR/SQSTM1/CTNNB1     9
##                    ID
## GO:0032355 GO:0032355
## GO:0048872 GO:0048872
## GO:1902893 GO:1902893
## GO:0061614 GO:0061614
## GO:0044772 GO:0044772
## GO:0043491 GO:0043491
##                                                                   Description
## GO:0032355                                              response to estradiol
## GO:0048872                                     homeostasis of number of cells
## GO:1902893                                  regulation of miRNA transcription
## GO:0061614                                                miRNA transcription
## GO:0044772                                mitotic cell cycle phase transition
## GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0032355     12/52 115/18888 2.424244e-16 7.435156e-13 3.299524e-13
## GO:0048872     15/52 322/18888 5.472674e-15 8.392346e-12 3.724299e-12
## GO:1902893      9/52  75/18888 4.794693e-13 4.161603e-10 1.846808e-10
## GO:0061614      9/52  76/18888 5.427588e-13 4.161603e-10 1.846808e-10
## GO:0044772     15/52 451/18888 7.411126e-13 4.545985e-10 2.017386e-10
## GO:0043491     13/52 299/18888 1.104312e-12 5.644877e-10 2.505046e-10
##                                                                                         geneID
## GO:0032355            ESR1/ERRFI1/IGF1R/CDKN1B/EZH2/NCOA3/EGFR/CASP3/STAT3/IGFBP2/ITGA2/CTNNB1
## GO:0048872   BAP1/G6PD/BCL2/KRAS/AKT1/BCL2L11/EZH2/XIAP/ETS1/FOXO3/AXL/CASP3/ANXA1/STAT3/GATA3
## GO:1902893                                     ESR1/NOTCH3/MYC/JUN/ETS1/FOXO3/EGFR/STAT3/GATA3
## GO:0061614                                     ESR1/NOTCH3/MYC/JUN/ETS1/FOXO3/EGFR/STAT3/GATA3
## GO:0044772 BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/CHEK1/CDKN1A/EGFR/FOXM1/CCNE2/RAD50
## GO:0043491                  ERRFI1/AKT1/IGF1R/PTEN/IRS1/FN1/AXL/PTK2/EGFR/STAT3/RET/GAB2/GATA3
##            Count
## GO:0032355    12
## GO:0048872    15
## GO:1902893     9
## GO:0061614     9
## GO:0044772    15
## GO:0043491    13
##                    ID                                       Description
## GO:0005925 GO:0005925                                    focal adhesion
## GO:0030055 GO:0030055                           cell-substrate junction
## GO:0070435 GO:0070435                                  Shc-EGFR complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0005899 GO:0005899                          insulin receptor complex
## GO:1902911 GO:1902911                            protein kinase complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0005925      9/52 421/19894 1.284721e-06 0.0001574755 9.601165e-05
## GO:0030055      9/52 431/19894 1.559164e-06 0.0001574755 9.601165e-05
## GO:0070435      2/52   2/19894 6.701178e-06 0.0003785405 2.307933e-04
## GO:0090571      3/52  15/19894 7.495851e-06 0.0003785405 2.307933e-04
## GO:0005899      2/52   4/19894 4.007244e-05 0.0014074824 8.581315e-04
## GO:1902911      5/52 150/19894 4.452637e-05 0.0014074824 8.581315e-04
##                                                       geneID Count
## GO:0005925 KRAS/SHC1/YWHAZ/PTK2/EGFR/CAV1/ANXA1/ITGA2/CTNNB1     9
## GO:0030055 KRAS/SHC1/YWHAZ/PTK2/EGFR/CAV1/ANXA1/ITGA2/CTNNB1     9
## GO:0070435                                         SHC1/EGFR     2
## GO:0090571                                  MYC/FOXO3/CTNNB1     3
## GO:0005899                                        IGF1R/IRS1     2
## GO:1902911                     CCND1/IGF1R/IRS1/CDKN1A/CCNE2     5
##                    ID
## GO:0043559 GO:0043559
## GO:0120283 GO:0120283
## GO:0043560 GO:0043560
## GO:0004707 GO:0004707
## GO:0005068 GO:0005068
## GO:0070064 GO:0070064
##                                                                Description
## GO:0043559                                                 insulin binding
## GO:0120283                         protein serine/threonine kinase binding
## GO:0043560                              insulin receptor substrate binding
## GO:0004707                                             MAP kinase activity
## GO:0005068 transmembrane receptor protein tyrosine kinase adaptor activity
## GO:0070064                                     proline-rich region binding
##            GeneRatio  BgRatio       pvalue    p.adjust      qvalue       geneID
## GO:0043559      2/24  5/18522 1.605294e-05 0.002809265 0.001165950 PIK3R1/IGF1R
## GO:0120283      2/24  7/18522 3.365781e-05 0.002945059 0.001222310   XIAP/MAPK8
## GO:0043560      2/24 13/18522 1.244222e-04 0.006307446 0.002617827 PIK3R1/IGF1R
## GO:0004707      2/24 16/18522 1.909646e-04 0.006307446 0.002617827  MAPK8/MAPK1
## GO:0005068      2/24 17/18522 2.162553e-04 0.006307446 0.002617827  PIK3R1/GAB2
## GO:0070064      2/24 17/18522 2.162553e-04 0.006307446 0.002617827   CCND1/YAP1
##            Count
## GO:0043559     2
## GO:0120283     2
## GO:0043560     2
## GO:0004707     2
## GO:0005068     2
## GO:0070064     2
##                    ID                                       Description
## GO:0071214 GO:0071214             cellular response to abiotic stimulus
## GO:0104004 GO:0104004       cellular response to environmental stimulus
## GO:0030099 GO:0030099                      myeloid cell differentiation
## GO:0042770 GO:0042770     signal transduction in response to DNA damage
## GO:0071496 GO:0071496            cellular response to external stimulus
## GO:1901990 GO:1901990 regulation of mitotic cell cycle phase transition
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0071214      8/24 334/18888 5.054206e-09 3.661773e-06 1.702470e-06
## GO:0104004      8/24 334/18888 5.054206e-09 3.661773e-06 1.702470e-06
## GO:0030099      8/24 439/18888 4.239931e-08 2.047887e-05 9.521249e-06
## GO:0042770      6/24 188/18888 1.040955e-07 3.770861e-05 1.753188e-05
## GO:0071496      7/24 335/18888 1.384829e-07 4.013234e-05 1.865875e-05
## GO:1901990      7/24 356/18888 2.092122e-07 5.052475e-05 2.349050e-05
##                                                    geneID Count
## GO:0071214 MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:0104004 MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:0030099  ETS1/MYH9/FOXO3/CASP8/PIK3R1/STAT5A/GAB2/FASN     8
## GO:0042770               BID/CDKN1A/FOXO3/ATM/CCND1/CHEK1     6
## GO:0071496     MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/IGF1R/MAPK1     7
## GO:1901990         ARID1A/BID/CDKN1A/ATM/CCND1/CHEK1/ANLN     7
##                    ID
## GO:0005826 GO:0005826
## GO:0070938 GO:0070938
## GO:0061695 GO:0061695
## GO:1902911 GO:1902911
## GO:0000307 GO:0000307
## GO:0005741 GO:0005741
##                                                               Description
## GO:0005826                                    actomyosin contractile ring
## GO:0070938                                               contractile ring
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:1902911                                         protein kinase complex
## GO:0000307             cyclin-dependent protein kinase holoenzyme complex
## GO:0005741                                   mitochondrial outer membrane
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0005826      2/24   4/19894 8.356555e-06 0.000977717 0.0005629679
## GO:0070938      2/24  10/19894 6.239748e-05 0.003650253 0.0021018098
## GO:0061695      4/24 308/19894 4.687667e-04 0.018281901 0.0105266907
## GO:1902911      3/24 150/19894 7.570559e-04 0.022143885 0.0127504154
## GO:0000307      2/24  56/19894 2.064262e-03 0.026838757 0.0154537153
## GO:0005741      3/24 219/19894 2.245291e-03 0.026838757 0.0154537153
##                               geneID Count
## GO:0005826                 MYH9/ANLN     2
## GO:0070938                 MYH9/ANLN     2
## GO:0061695 CDKN1A/CCND1/PIK3R1/IGF1R     4
## GO:1902911        CDKN1A/CCND1/IGF1R     3
## GO:0000307              CDKN1A/CCND1     2
## GO:0005741           BID/FOXO3/CASP8     3
##                    ID                              Description GeneRatio
## GO:0106310 GO:0106310           protein serine kinase activity      5/25
## GO:0004707 GO:0004707                      MAP kinase activity      2/25
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/25
## GO:0070064 GO:0070064              proline-rich region binding      2/25
## GO:0042826 GO:0042826              histone deacetylase binding      3/25
## GO:0045296 GO:0045296                         cadherin binding      4/25
##              BgRatio       pvalue   p.adjust      qvalue
## GO:0106310 363/18522 0.0001081824 0.01192286 0.004945963
## GO:0004707  16/18522 0.0002074657 0.01192286 0.004945963
## GO:0004674 427/18522 0.0002308630 0.01192286 0.004945963
## GO:0070064  17/18522 0.0002349333 0.01192286 0.004945963
## GO:0042826 128/18522 0.0006634074 0.01766587 0.007328335
## GO:0045296 333/18522 0.0009629296 0.01766587 0.007328335
##                               geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
## GO:0045296     HSPA1A/MYH9/ANLN/FASN     4
##                    ID                           Description GeneRatio   BgRatio
## GO:0010631 GO:0010631             epithelial cell migration      9/25 375/18888
## GO:0090132 GO:0090132                  epithelium migration      9/25 378/18888
## GO:0090130 GO:0090130                      tissue migration      9/25 383/18888
## GO:0030099 GO:0030099          myeloid cell differentiation      9/25 439/18888
## GO:0062197 GO:0062197  cellular response to chemical stress      8/25 311/18888
## GO:0071214 GO:0071214 cellular response to abiotic stimulus      8/25 334/18888
##                  pvalue     p.adjust       qvalue
## GO:0010631 6.722030e-10 5.415358e-07 2.272198e-07
## GO:0090132 7.210613e-10 5.415358e-07 2.272198e-07
## GO:0090130 8.094706e-10 5.415358e-07 2.272198e-07
## GO:0030099 2.679241e-09 1.344309e-06 5.640507e-07
## GO:0062197 4.187089e-09 1.680697e-06 7.051939e-07
## GO:0071214 7.318853e-09 2.016998e-06 8.463004e-07
##                                                        geneID Count
## GO:0010631    AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090132    AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090130    AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0030099 HSPA1A/MTOR/MYH9/FOXO3/CASP8/ETS1/STAT5A/G6PD/FASN     9
## GO:0062197        HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1/G6PD     8
## GO:0071214        MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                         Description GeneRatio   BgRatio
## GO:0005925 GO:0005925                      focal adhesion      7/25 421/19894
## GO:0030055 GO:0030055             cell-substrate junction      7/25 431/19894
## GO:0005826 GO:0005826         actomyosin contractile ring      2/25   4/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane      4/25 161/19894
## GO:0070938 GO:0070938                    contractile ring      2/25  10/19894
## GO:0098562 GO:0098562        cytoplasmic side of membrane      4/25 199/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.252929e-07 4.757557e-05 2.696591e-05
## GO:0030055 7.319319e-07 4.757557e-05 2.696591e-05
## GO:0005826 9.082603e-06 3.935795e-04 2.230815e-04
## GO:0009898 4.578147e-05 1.487898e-03 8.433429e-04
## GO:0070938 6.780516e-05 1.762934e-03 9.992340e-04
## GO:0098562 1.042248e-04 2.258203e-03 1.279953e-03
##                                            geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0005826                              MYH9/ANLN     2
## GO:0009898                    MYH9/PTEN/KRAS/G6PD     4
## GO:0070938                              MYH9/ANLN     2
## GO:0098562                    MYH9/PTEN/KRAS/G6PD     4
##                    ID                              Description GeneRatio
## GO:0019902 GO:0019902                      phosphatase binding      5/28
## GO:0001221 GO:0001221        transcription coregulator binding      4/28
## GO:0030235 GO:0030235 nitric-oxide synthase regulator activity      2/28
## GO:0001222 GO:0001222        transcription corepressor binding      3/28
## GO:0019903 GO:0019903              protein phosphatase binding      4/28
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      6/28
##              BgRatio       pvalue    p.adjust       qvalue
## GO:0019902 189/18522 8.521722e-06 0.001704344 0.0007086485
## GO:0001221 114/18522 2.486433e-05 0.002217794 0.0009221356
## GO:0030235   7/18522 4.606338e-05 0.002217794 0.0009221356
## GO:0001222  47/18522 4.798130e-05 0.002217794 0.0009221356
## GO:0019903 142/18522 5.876068e-05 0.002217794 0.0009221356
## GO:0140297 478/18522 6.653383e-05 0.002217794 0.0009221356
##                                       geneID Count
## GO:0019902        MET/BCL2/PTK2/MAPK1/CTNNB1     5
## GO:0001221            ESR1/FOXO3/ETS1/CTNNB1     4
## GO:0030235                         ESR1/AKT1     2
## GO:0001222                  ESR1/ETS1/CTNNB1     3
## GO:0019903              MET/BCL2/PTK2/CTNNB1     4
## GO:0140297 ESR1/BCL2/ETS1/STAT5A/YAP1/CTNNB1     6
##                    ID                            Description GeneRatio
## GO:0048732 GO:0048732                      gland development     11/28
## GO:0001667 GO:0001667          ameboidal-type cell migration     10/28
## GO:0043523 GO:0043523 regulation of neuron apoptotic process      8/28
## GO:0033002 GO:0033002              muscle cell proliferation      8/28
## GO:0010631 GO:0010631              epithelial cell migration      9/28
## GO:0090132 GO:0090132                   epithelium migration      9/28
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0048732 449/18888 1.809829e-11 4.224140e-08 1.600270e-08
## GO:0001667 498/18888 1.271623e-09 8.646514e-07 3.275638e-07
## GO:0043523 244/18888 1.719699e-09 8.646514e-07 3.275638e-07
## GO:0033002 251/18888 2.149085e-09 8.646514e-07 3.275638e-07
## GO:0010631 375/18888 2.155959e-09 8.646514e-07 3.275638e-07
## GO:0090132 378/18888 2.311658e-09 8.646514e-07 3.275638e-07
##                                                                 geneID Count
## GO:0048732 ESR1/MET/BCL2/CCND1/AKT1/ATM/STAT5A/MAPK1/ITGA2/CTNNB1/TGM2    11
## GO:0001667          MET/AKT1/MYH9/PTEN/PTK2/ETS1/STAT5A/FN1/ANLN/ITGA2    10
## GO:0043523                 G6PD/BCL2/KRAS/CCND1/FOXO3/ATM/CASP8/CTNNB1     8
## GO:0033002             NOTCH3/AKT1/IGF1R/CDKN1A/PTEN/YAP1/ITGA2/CTNNB1     8
## GO:0010631              MET/AKT1/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090132              MET/AKT1/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
##                    ID                         Description GeneRatio   BgRatio
## GO:0005925 GO:0005925                      focal adhesion      7/28 421/19894
## GO:0030055 GO:0030055             cell-substrate junction      7/28 431/19894
## GO:0005826 GO:0005826         actomyosin contractile ring      2/28   4/19894
## GO:0005938 GO:0005938                         cell cortex      5/28 309/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane      4/28 161/19894
## GO:0070938 GO:0070938                    contractile ring      2/28  10/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 1.457953e-06 0.0001448678 7.445221e-05
## GO:0030055 1.704328e-06 0.0001448678 7.445221e-05
## GO:0005826 1.144178e-05 0.0006483674 3.332167e-04
## GO:0005938 6.414545e-05 0.0024186976 1.243046e-03
## GO:0009898 7.271284e-05 0.0024186976 1.243046e-03
## GO:0070938 8.536580e-05 0.0024186976 1.243046e-03
##                                            geneID Count
## GO:0005925 KRAS/MYH9/PTK2/MAPK1/ITGA2/CTNNB1/TGM2     7
## GO:0030055 KRAS/MYH9/PTK2/MAPK1/ITGA2/CTNNB1/TGM2     7
## GO:0005826                              MYH9/ANLN     2
## GO:0005938             AKT1/MYH9/PTK2/ANLN/CTNNB1     5
## GO:0009898                    G6PD/KRAS/MYH9/PTEN     4
## GO:0070938                              MYH9/ANLN     2
##                    ID
## GO:0140313 GO:0140313
## GO:0019903 GO:0019903
## GO:0019887 GO:0019887
## GO:0016538 GO:0016538
## GO:0004714 GO:0004714
## GO:0030235 GO:0030235
##                                                                    Description
## GO:0140313                                     molecular sequestering activity
## GO:0019903                                         protein phosphatase binding
## GO:0019887                                   protein kinase regulator activity
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0004714             transmembrane receptor protein tyrosine kinase activity
## GO:0030235                            nitric-oxide synthase regulator activity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0140313      6/53  49/18522 5.217115e-09 1.779036e-06 8.292468e-07
## GO:0019903      7/53 142/18522 1.540591e-07 2.590235e-05 1.207364e-05
## GO:0019887      8/53 232/18522 2.929329e-07 2.590235e-05 1.207364e-05
## GO:0016538      5/53  50/18522 3.038399e-07 2.590235e-05 1.207364e-05
## GO:0004714      5/53  60/18522 7.664643e-07 3.499023e-05 1.630969e-05
## GO:0030235      3/53   7/18522 7.680745e-07 3.499023e-05 1.630969e-05
##                                                    geneID Count
## GO:0140313            YWHAZ/CDKN1A/CAV1/STAT3/SQSTM1/LCN2     6
## GO:0019903          MET/BCL2/CDKN1B/MAPK8/PTK2/EGFR/STAT3     7
## GO:0019887 CCND1/AKT1/CDKN1B/CDKN1A/EGFR/CAV1/CASP3/CCNE2     8
## GO:0016538                CCND1/CDKN1B/CDKN1A/CASP3/CCNE2     5
## GO:0004714                         MET/IGF1R/AXL/EGFR/RET     5
## GO:0030235                                 ESR1/AKT1/EGFR     3
##                    ID                                         Description
## GO:0048872 GO:0048872                      homeostasis of number of cells
## GO:0032355 GO:0032355                               response to estradiol
## GO:0044772 GO:0044772                 mitotic cell cycle phase transition
## GO:0000082 GO:0000082               G1/S transition of mitotic cell cycle
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843                    cell cycle G1/S phase transition
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0048872     15/53 322/18888 7.516594e-15 2.210630e-11 1.020674e-11
## GO:0032355     11/53 115/18888 1.607967e-14 2.364516e-11 1.091725e-11
## GO:0044772     16/53 451/18888 5.662713e-14 4.627298e-11 2.136479e-11
## GO:0000082     13/53 234/18888 6.293503e-14 4.627298e-11 2.136479e-11
## GO:2000045     12/53 185/18888 1.023246e-13 6.018730e-11 2.778919e-11
## GO:0044843     13/53 262/18888 2.684370e-13 1.315789e-10 6.075154e-11
##                                                                                             geneID
## GO:0048872       BAP1/G6PD/BCL2/KRAS/AKT1/BCL2L11/EZH2/XIAP/ETS1/FOXO3/AXL/CASP3/ANXA1/STAT3/GATA3
## GO:0032355                       ESR1/ERRFI1/IGF1R/CDKN1B/EZH2/NCOA3/EGFR/CASP3/STAT3/IGFBP2/ITGA2
## GO:0044772 BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/ATM/CHEK1/CDKN1A/EGFR/FOXM1/CCNE2/RAD50
## GO:0000082                   BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/ATM/CDKN1A/EGFR/CCNE2
## GO:2000045                       BCL2/CCND1/AKT1/PTEN/CDKN1B/EZH2/ARID1A/BID/ATM/CDKN1A/EGFR/CCNE2
## GO:0044843                   BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/ATM/CDKN1A/EGFR/CCNE2
##            Count
## GO:0048872    15
## GO:0032355    11
## GO:0044772    16
## GO:0000082    13
## GO:2000045    12
## GO:0044843    13
##                    ID                  Description GeneRatio   BgRatio
## GO:0070435 GO:0070435             Shc-EGFR complex      2/53   2/19894
## GO:0005925 GO:0005925               focal adhesion      8/53 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      8/53 431/19894
## GO:0005899 GO:0005899     insulin receptor complex      2/53   4/19894
## GO:1902911 GO:1902911       protein kinase complex      5/53 150/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      5/53 219/19894
##                  pvalue    p.adjust       qvalue
## GO:0070435 6.963969e-06 0.001018184 0.0006623315
## GO:0005925 1.449096e-05 0.001018184 0.0006623315
## GO:0030055 1.716041e-05 0.001018184 0.0006623315
## GO:0005899 4.164111e-05 0.001739692 0.0011316746
## GO:1902911 4.886777e-05 0.001739692 0.0011316746
## GO:0005741 2.883549e-04 0.007860523 0.0051132908
##                                                geneID Count
## GO:0070435                                  SHC1/EGFR     2
## GO:0005925 KRAS/SHC1/PTK2/YWHAZ/EGFR/CAV1/ANXA1/ITGA2     8
## GO:0030055 KRAS/SHC1/PTK2/YWHAZ/EGFR/CAV1/ANXA1/ITGA2     8
## GO:0005899                                 IGF1R/IRS1     2
## GO:1902911              CCND1/IGF1R/IRS1/CDKN1A/CCNE2     5
## GO:0005741                BCL2/KRAS/BCL2L11/BID/FOXO3     5
##                    ID
## GO:0140297 GO:0140297
## GO:0061629 GO:0061629
## GO:0001221 GO:0001221
## GO:0019903 GO:0019903
## GO:0019902 GO:0019902
## GO:0097718 GO:0097718
##                                                                    Description
## GO:0140297                            DNA-binding transcription factor binding
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0001221                                   transcription coregulator binding
## GO:0019903                                         protein phosphatase binding
## GO:0019902                                                 phosphatase binding
## GO:0097718                                  disordered domain specific binding
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0140297     10/27 478/18522 6.791959e-10 1.324432e-07 6.291499e-08
## GO:0061629      7/27 343/18522 4.535843e-07 3.808236e-05 1.809041e-05
## GO:0001221      5/27 114/18522 5.858824e-07 3.808236e-05 1.809041e-05
## GO:0019903      5/27 142/18522 1.739208e-06 8.478639e-05 4.027639e-05
## GO:0019902      5/27 189/18522 7.058179e-06 2.752690e-04 1.307621e-04
## GO:0097718      3/27  32/18522 1.332054e-05 4.329175e-04 2.056504e-04
##                                                            geneID Count
## GO:0140297 ESR1/BCL2/RB1/ETS1/ARID1A/YWHAZ/NCOA3/GATA3/CTNNB1/VHL    10
## GO:0061629                ESR1/RB1/ETS1/ARID1A/NCOA3/GATA3/CTNNB1     7
## GO:0001221                           ESR1/ETS1/FOXO3/GATA3/CTNNB1     5
## GO:0019903                             MET/BCL2/MAPK8/CDH2/CTNNB1     5
## GO:0019902                             MET/BCL2/MAPK8/CDH2/CTNNB1     5
## GO:0097718                                       RB1/NCOA3/CTNNB1     3
##                    ID                                     Description GeneRatio
## GO:0051402 GO:0051402                        neuron apoptotic process     10/27
## GO:0048872 GO:0048872                  homeostasis of number of cells     10/27
## GO:1904019 GO:1904019               epithelial cell apoptotic process      7/27
## GO:0030099 GO:0030099                    myeloid cell differentiation      9/27
## GO:1904035 GO:1904035 regulation of epithelial cell apoptotic process      6/27
## GO:0043523 GO:0043523          regulation of neuron apoptotic process      7/27
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0051402 292/18888 4.472956e-12 9.880759e-09 4.016243e-09
## GO:0048872 322/18888 1.177305e-11 1.300333e-08 5.285479e-09
## GO:1904019 147/18888 1.167740e-09 8.598459e-07 3.495025e-07
## GO:0030099 439/18888 5.897771e-09 3.257044e-06 1.323894e-06
## GO:1904035 115/18888 1.191071e-08 5.262152e-06 2.138913e-06
## GO:0043523 244/18888 3.924792e-08 1.444978e-05 5.873417e-06
##                                                          geneID Count
## GO:0051402 G6PD/BCL2/KRAS/CCND1/RB1/XIAP/BID/FOXO3/GATA3/CTNNB1    10
## GO:0048872   G6PD/BCL2/KRAS/AKT1/RB1/XIAP/ETS1/FOXO3/CDH2/GATA3    10
## GO:1904019                  ESR1/BCL2/IGF1R/RB1/BID/FOXO3/GATA3     7
## GO:0030099     G6PD/RB1/ETS1/FOXO3/GAB2/GATA3/CTNNB1/RBM15/FASN     9
## GO:1904035                      ESR1/BCL2/IGF1R/RB1/FOXO3/GATA3     6
## GO:0043523              G6PD/BCL2/KRAS/CCND1/FOXO3/GATA3/CTNNB1     7
##                    ID                                       Description
## GO:0005916 GO:0005916                                   fascia adherens
## GO:0017053 GO:0017053                   transcription repressor complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0005741 GO:0005741                      mitochondrial outer membrane
## GO:0031968 GO:0031968                          organelle outer membrane
## GO:0019867 GO:0019867                                    outer membrane
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0005916      2/27   9/19894 6.348477e-05 0.006782767 0.002650363
## GO:0017053      3/27  77/19894 1.525165e-04 0.006782767 0.002650363
## GO:0090571      2/27  15/19894 1.842356e-04 0.006782767 0.002650363
## GO:0005741      4/27 219/19894 2.055384e-04 0.006782767 0.002650363
## GO:0031968      4/27 248/19894 3.301165e-04 0.007487277 0.002925650
## GO:0019867      4/27 250/19894 3.403308e-04 0.007487277 0.002925650
##                         geneID Count
## GO:0005916         CDH2/CTNNB1     2
## GO:0017053  CCND1/FOXO3/CTNNB1     3
## GO:0090571        FOXO3/CTNNB1     2
## GO:0005741 BCL2/KRAS/BID/FOXO3     4
## GO:0031968 BCL2/KRAS/BID/FOXO3     4
## GO:0019867 BCL2/KRAS/BID/FOXO3     4
##                    ID                              Description GeneRatio
## GO:0005178 GO:0005178                         integrin binding      4/23
## GO:0106310 GO:0106310           protein serine kinase activity      5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/23
## GO:0004707 GO:0004707                      MAP kinase activity      2/23
## GO:0070064 GO:0070064              proline-rich region binding      2/23
## GO:0042826 GO:0042826              histone deacetylase binding      3/23
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0005178 157/18522 3.880147e-05 0.006191422 0.002457948
## GO:0106310 363/18522 7.075911e-05 0.006191422 0.002457948
## GO:0004674 427/18522 1.518718e-04 0.006941937 0.002755897
## GO:0004707  16/18522 1.751391e-04 0.006941937 0.002755897
## GO:0070064  17/18522 1.983411e-04 0.006941937 0.002755897
## GO:0042826 128/18522 5.160029e-04 0.015050083 0.005974770
##                               geneID Count
## GO:0005178       MYH9/PTK2/ITGA2/FN1     4
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
##                    ID                                 Description GeneRatio
## GO:0001667 GO:0001667               ameboidal-type cell migration     10/23
## GO:0010631 GO:0010631                   epithelial cell migration      9/23
## GO:0090132 GO:0090132                        epithelium migration      9/23
## GO:0090130 GO:0090130                            tissue migration      9/23
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/23
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0001667 498/18888 1.248213e-10 1.608487e-07 6.288568e-08
## GO:0010631 375/18888 2.784961e-10 1.608487e-07 6.288568e-08
## GO:0090132 378/18888 2.988249e-10 1.608487e-07 6.288568e-08
## GO:0090130 383/18888 3.356258e-10 1.608487e-07 6.288568e-08
## GO:0071214 334/18888 3.421872e-09 1.093288e-06 4.274339e-07
## GO:0104004 334/18888 3.421872e-09 1.093288e-06 4.274339e-07
##                                                         geneID Count
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2/FN1    10
## GO:0010631     AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090132     AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090130     AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0071214         MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004         MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                  Description GeneRatio   BgRatio
## GO:0005925 GO:0005925               focal adhesion      6/23 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      6/23 431/19894
## GO:0005826 GO:0005826  actomyosin contractile ring      2/23   4/19894
## GO:0070938 GO:0070938             contractile ring      2/23  10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      4/23 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      4/23 248/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.447048e-06 0.0003319632 0.0001827814
## GO:0030055 7.373490e-06 0.0003319632 0.0001827814
## GO:0005826 7.660689e-06 0.0003319632 0.0001827814
## GO:0070938 5.721303e-05 0.0018594235 0.0010238121
## GO:0005741 1.073470e-04 0.0027910215 0.0015367568
## GO:0031968 1.732117e-04 0.0033173797 0.0018265734
##                                       geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2     6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2     6
## GO:0005826                         MYH9/ANLN     2
## GO:0070938                         MYH9/ANLN     2
## GO:0005741             MTOR/FOXO3/CASP8/KRAS     4
## GO:0031968             MTOR/FOXO3/CASP8/KRAS     4
##                    ID                                        Description
## GO:0106310 GO:0106310                     protein serine kinase activity
## GO:0004674 GO:0004674           protein serine/threonine kinase activity
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0003925 GO:0003925                                 G protein activity
## GO:0004860 GO:0004860                  protein kinase inhibitor activity
## GO:0001156 GO:0001156  TFIIIC-class transcription factor complex binding
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0106310      4/15 363/18522 0.0001669197 0.01507202 0.004898006
## GO:0004674      4/15 427/18522 0.0003106963 0.01507202 0.004898006
## GO:0030291      2/15  37/18522 0.0004010778 0.01507202 0.004898006
## GO:0003925      2/15  45/18522 0.0005939699 0.01507202 0.004898006
## GO:0004860      2/15  73/18522 0.0015562116 0.01507202 0.004898006
## GO:0001156      1/15   2/18522 0.0016190833 0.01507202 0.004898006
##                         geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM     4
## GO:0004674 AKT1/MTOR/MAPK8/ATM     4
## GO:0030291         AKT1/CDKN1A     2
## GO:0003925           KRAS/NRAS     2
## GO:0004860         AKT1/CDKN1A     2
## GO:0001156                MTOR     1
##                    ID                                      Description
## GO:0010632 GO:0010632          regulation of epithelial cell migration
## GO:0010634 GO:0010634 positive regulation of epithelial cell migration
## GO:0010631 GO:0010631                        epithelial cell migration
## GO:0090132 GO:0090132                             epithelium migration
## GO:0090130 GO:0090130                                 tissue migration
## GO:0009408 GO:0009408                                 response to heat
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0010632      7/15 298/18888 1.309993e-09 2.154939e-06 7.460068e-07
## GO:0010634      6/15 177/18888 2.902927e-09 2.387657e-06 8.265701e-07
## GO:0010631      7/15 375/18888 6.453146e-09 2.456663e-06 8.504588e-07
## GO:0090132      7/15 378/18888 6.818674e-09 2.456663e-06 8.504588e-07
## GO:0090130      7/15 383/18888 7.467060e-09 2.456663e-06 8.504588e-07
## GO:0009408      5/15 104/18888 1.320196e-08 3.619538e-06 1.253028e-06
##                                           geneID Count
## GO:0010632 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0010634      AKT1/MTOR/PTK2/ETS1/STAT5A/ITGA2     6
## GO:0010631 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0090132 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0090130 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0009408           HSPA1A/AKT1/MTOR/ATM/CDKN1A     5
##                    ID                         Description GeneRatio   BgRatio
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane      3/15 161/19894
## GO:0005925 GO:0005925                      focal adhesion      4/15 421/19894
## GO:0030055 GO:0030055             cell-substrate junction      4/15 431/19894
## GO:0098562 GO:0098562        cytoplasmic side of membrane      3/15 199/19894
## GO:0070557 GO:0070557                    PCNA-p21 complex      1/15   2/19894
## GO:0034666 GO:0034666       integrin alpha2-beta1 complex      1/15   3/19894
##                  pvalue    p.adjust      qvalue                 geneID Count
## GO:0009898 0.0002203815 0.006051504 0.003701489         PTEN/KRAS/G6PD     3
## GO:0005925 0.0002242685 0.006051504 0.003701489 HSPA1A/KRAS/PTK2/ITGA2     4
## GO:0030055 0.0002453312 0.006051504 0.003701489 HSPA1A/KRAS/PTK2/ITGA2     4
## GO:0098562 0.0004105210 0.007594638 0.004645369         PTEN/KRAS/G6PD     3
## GO:0070557 0.0015074617 0.022310434 0.013646496                 CDKN1A     1
## GO:0034666 0.0022603970 0.027878229 0.017052118                  ITGA2     1
##                    ID
## GO:0120283 GO:0120283
## GO:0140297 GO:0140297
## GO:0016747 GO:0016747
## GO:0030374 GO:0030374
## GO:0003713 GO:0003713
## GO:0061629 GO:0061629
##                                                                           Description
## GO:0120283                                    protein serine/threonine kinase binding
## GO:0140297                                   DNA-binding transcription factor binding
## GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
## GO:0030374                                      nuclear receptor coactivator activity
## GO:0003713                                         transcription coactivator activity
## GO:0061629        RNA polymerase II-specific DNA-binding transcription factor binding
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0120283      2/11   7/18522 6.722891e-06 0.0006991806 0.0002689156
## GO:0140297      4/11 478/18522 1.251440e-04 0.0065074889 0.0025028804
## GO:0016747      3/11 226/18522 2.751516e-04 0.0072644370 0.0027940142
## GO:0030374      2/11  55/18522 4.680676e-04 0.0072644370 0.0027940142
## GO:0003713      3/11 271/18522 4.685463e-04 0.0072644370 0.0027940142
## GO:0061629      3/11 343/18522 9.301306e-04 0.0072644370 0.0027940142
##                              geneID Count
## GO:0120283               XIAP/MAPK8     2
## GO:0140297 ETS1/ARID1A/STAT5A/NCOA3     4
## GO:0016747          NCOA3/TGM2/FASN     3
## GO:0030374               ETS1/NCOA3     2
## GO:0003713        ETS1/ARID1A/NCOA3     3
## GO:0061629        ETS1/ARID1A/NCOA3     3
##                    ID                                         Description
## GO:0030099 GO:0030099                        myeloid cell differentiation
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0071353 GO:0071353                  cellular response to interleukin-4
## GO:0070670 GO:0070670                           response to interleukin-4
## GO:1902806 GO:1902806      regulation of cell cycle G1/S phase transition
## GO:0030851 GO:0030851                         granulocyte differentiation
##            GeneRatio   BgRatio       pvalue   p.adjust     qvalue
## GO:0030099      4/11 439/18888 0.0000834442 0.02183444 0.01068352
## GO:2000045      3/11 185/18888 0.0001439698 0.02183444 0.01068352
## GO:0071353      2/11  34/18888 0.0001712343 0.02183444 0.01068352
## GO:0070670      2/11  37/18888 0.0002030898 0.02183444 0.01068352
## GO:1902806      3/11 211/18888 0.0002122639 0.02183444 0.01068352
## GO:0030851      2/11  41/18888 0.0002497329 0.02183444 0.01068352
##                           geneID Count
## GO:0030099 ETS1/STAT5A/GAB2/FASN     4
## GO:2000045     ARID1A/BID/CDKN1A     3
## GO:0071353           STAT5A/FASN     2
## GO:0070670           STAT5A/FASN     2
## GO:1902806     ARID1A/BID/CDKN1A     3
## GO:0030851           STAT5A/FASN     2
##                    ID      Description GeneRatio  BgRatio      pvalue
## GO:0070557 GO:0070557 PCNA-p21 complex      1/11  2/19894 0.001105583
## GO:0042587 GO:0042587 glycogen granule      1/11  6/19894 0.003313416
## GO:0097441 GO:0097441   basal dendrite      1/11  6/19894 0.003313416
## GO:0140092 GO:0140092     bBAF complex      1/11 10/19894 0.005516813
## GO:0035060 GO:0035060   brahma complex      1/11 14/19894 0.007715780
## GO:0071564 GO:0071564    npBAF complex      1/11 14/19894 0.007715780
##              p.adjust     qvalue geneID Count
## GO:0070557 0.02871628 0.01976424 CDKN1A     1
## GO:0042587 0.02871628 0.01976424   FASN     1
## GO:0097441 0.02871628 0.01976424  MAPK8     1
## GO:0140092 0.03273625 0.02253102 ARID1A     1
## GO:0035060 0.03273625 0.02253102 ARID1A     1
## GO:0071564 0.03273625 0.02253102 ARID1A     1
##                    ID
## GO:0032143 GO:0032143
## GO:0019902 GO:0019902
## GO:0016538 GO:0016538
## GO:0001221 GO:0001221
## GO:0140297 GO:0140297
## GO:0005123 GO:0005123
##                                                                    Description
## GO:0032143                                    single thymine insertion binding
## GO:0019902                                                 phosphatase binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0001221                                   transcription coregulator binding
## GO:0140297                            DNA-binding transcription factor binding
## GO:0005123                                              death receptor binding
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0032143      2/45   2/18522 5.771821e-06 0.0005925934 0.0002755751
## GO:0019902      6/45 189/18522 6.100384e-06 0.0005925934 0.0002755751
## GO:0016538      4/45  50/18522 6.451683e-06 0.0005925934 0.0002755751
## GO:0001221      5/45 114/18522 8.117718e-06 0.0005925934 0.0002755751
## GO:0140297      8/45 478/18522 1.727807e-05 0.0006310362 0.0002934523
## GO:0005123      3/45  21/18522 1.728589e-05 0.0006310362 0.0002934523
##                                                  geneID Count
## GO:0032143                                    MSH6/MSH2     2
## GO:0019902             MAPK8/PTK2/MAPK1/BCL2/CTNNB1/PXN     6
## GO:0016538                     CDKN1A/CCNE2/CCND1/CASP3     4
## GO:0001221                   ETS1/FOXO3/EZH2/MYC/CTNNB1     5
## GO:0140297 ETS1/ARID1A/PARP1/NCOA3/YAP1/BCL2/MYC/CTNNB1     8
## GO:0005123                              BID/CASP8/CASP3     3
##                    ID                                 Description GeneRatio
## GO:0051402 GO:0051402                    neuron apoptotic process     15/45
## GO:0043523 GO:0043523      regulation of neuron apoptotic process     13/45
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     13/45
## GO:0104004 GO:0104004 cellular response to environmental stimulus     13/45
## GO:0009411 GO:0009411                              response to UV     10/45
## GO:0009314 GO:0009314                       response to radiation     13/45
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0051402 292/18888 1.093198e-16 2.908999e-13 1.264657e-13
## GO:0043523 244/18888 1.025006e-14 1.363771e-11 5.928853e-12
## GO:0071214 334/18888 5.749508e-13 3.824860e-10 1.662818e-10
## GO:0104004 334/18888 5.749508e-13 3.824860e-10 1.662818e-10
## GO:0009411 154/18888 2.414609e-12 1.285055e-09 5.586643e-10
## GO:0009314 431/18888 1.429178e-11 5.716190e-09 2.485054e-09
##                                                                                          geneID
## GO:0051402 XIAP/BID/FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/BCL2/CASP3/BCL2L11/PIK3CA/MSH2/CTNNB1/G6PD
## GO:0043523          FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/BCL2/CASP3/BCL2L11/PIK3CA/MSH2/CTNNB1/G6PD
## GO:0071214           MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/RAB11B/YAP1/ITGA2/MYC/CASP3/PIK3CA
## GO:0104004           MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/RAB11B/YAP1/ITGA2/MYC/CASP3/PIK3CA
## GO:0009411                             MAPK8/CDKN1A/PARP1/CCND1/BCL2/MYC/CASP3/MSH6/MSH2/PRKAA1
## GO:0009314               MAPK8/CDKN1A/ATM/KRAS/PARP1/CCND1/YAP1/BCL2/MYC/CASP3/MSH6/MSH2/PRKAA1
##            Count
## GO:0051402    15
## GO:0043523    13
## GO:0071214    13
## GO:0104004    13
## GO:0009411    10
## GO:0009314    13
##                    ID                                       Description
## GO:0005925 GO:0005925                                    focal adhesion
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0030055 GO:0030055                           cell-substrate junction
## GO:0032301 GO:0032301                                 MutSalpha complex
## GO:0005938 GO:0005938                                       cell cortex
## GO:0030027 GO:0030027                                     lamellipodium
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0005925      8/45 421/19894 4.085587e-06 0.000230887 0.0001268965
## GO:0090571      3/45  15/19894 4.828225e-06 0.000230887 0.0001268965
## GO:0030055      8/45 431/19894 4.855524e-06 0.000230887 0.0001268965
## GO:0032301      2/45   2/19894 5.003142e-06 0.000230887 0.0001268965
## GO:0005938      7/45 309/19894 5.574616e-06 0.000230887 0.0001268965
## GO:0030027      6/45 203/19894 6.129745e-06 0.000230887 0.0001268965
##                                                 geneID Count
## GO:0005925 MYH9/KRAS/PTK2/MAPK1/ITGA2/CTNNB1/YWHAB/PXN     8
## GO:0090571                            FOXO3/MYC/CTNNB1     3
## GO:0030055 MYH9/KRAS/PTK2/MAPK1/ITGA2/CTNNB1/YWHAB/PXN     8
## GO:0032301                                   MSH6/MSH2     2
## GO:0005938          MYH9/PTK2/ANLN/CDH1/CTNNB1/PXN/NF2     7
## GO:0030027            CASP8/PIK3CA/CDH1/CTNNB1/PXN/NF2     6
##                    ID                        Description GeneRatio   BgRatio
## GO:0019903 GO:0019903        protein phosphatase binding      4/17 142/18522
## GO:0019902 GO:0019902                phosphatase binding      4/17 189/18522
## GO:0045294 GO:0045294              alpha-catenin binding      2/17  10/18522
## GO:0042826 GO:0042826        histone deacetylase binding      3/17 128/18522
## GO:0106310 GO:0106310     protein serine kinase activity      4/17 363/18522
## GO:0097718 GO:0097718 disordered domain specific binding      2/17  32/18522
##                  pvalue    p.adjust       qvalue                 geneID Count
## GO:0019903 7.292870e-06 0.001115809 0.0003224216 MAPK8/PTK2/CDH2/CTNNB1     4
## GO:0019902 2.252767e-05 0.001723367 0.0004979802 MAPK8/PTK2/CDH2/CTNNB1     4
## GO:0045294 3.552653e-05 0.001811853 0.0005235488            CDH2/CTNNB1     2
## GO:0042826 2.042216e-04 0.007811478 0.0022571866     HSPA1A/MAPK8/CCND1     3
## GO:0106310 2.821457e-04 0.008633658 0.0024947619    AKT1/MTOR/MAPK8/ATM     4
## GO:0097718 3.869583e-04 0.009867436 0.0028512715          HSPA1A/CTNNB1     2
##                    ID                                      Description
## GO:0010632 GO:0010632          regulation of epithelial cell migration
## GO:0001667 GO:0001667                    ameboidal-type cell migration
## GO:0010634 GO:0010634 positive regulation of epithelial cell migration
## GO:0010631 GO:0010631                        epithelial cell migration
## GO:0090132 GO:0090132                             epithelium migration
## GO:0035995 GO:0035995                      detection of muscle stretch
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0010632      7/17 298/18888 3.853183e-09 4.231961e-06 1.410004e-06
## GO:0001667      8/17 498/18888 4.356110e-09 4.231961e-06 1.410004e-06
## GO:0010634      6/17 177/18888 7.067261e-09 4.577230e-06 1.525041e-06
## GO:0010631      7/17 375/18888 1.884459e-08 6.048023e-06 2.015079e-06
## GO:0090132      7/17 378/18888 1.990641e-08 6.048023e-06 2.015079e-06
## GO:0035995      3/17   7/18888 2.114819e-08 6.048023e-06 2.015079e-06
##                                                geneID Count
## GO:0010632      AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0001667 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2/CDH2     8
## GO:0010634           AKT1/MTOR/PTK2/ETS1/STAT5A/ITGA2     6
## GO:0010631      AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0090132      AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0035995                           PTK2/CDH2/CTNNB1     3
##                    ID                  Description GeneRatio   BgRatio
## GO:0005925 GO:0005925               focal adhesion      6/17 421/19894
## GO:0030055 GO:0030055      cell-substrate junction      6/17 431/19894
## GO:0005916 GO:0005916              fascia adherens      2/17   9/19894
## GO:0005938 GO:0005938                  cell cortex      4/17 309/19894
## GO:0016327 GO:0016327 apicolateral plasma membrane      2/17  23/19894
## GO:0016342 GO:0016342              catenin complex      2/17  31/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 8.803502e-07 6.561649e-05 0.0000276280
## GO:0030055 1.009484e-06 6.561649e-05 0.0000276280
## GO:0005916 2.465588e-05 1.068421e-03 0.0004498616
## GO:0005938 1.157984e-04 3.763448e-03 0.0015846097
## GO:0016327 1.720609e-04 4.473583e-03 0.0018836140
## GO:0016342 3.149696e-04 6.824342e-03 0.0028734070
##                                        geneID Count
## GO:0005925 HSPA1A/KRAS/PTK2/ITGA2/CDH2/CTNNB1     6
## GO:0030055 HSPA1A/KRAS/PTK2/ITGA2/CDH2/CTNNB1     6
## GO:0005916                        CDH2/CTNNB1     2
## GO:0005938              AKT1/PTK2/CDH2/CTNNB1     4
## GO:0016327                        CDH2/CTNNB1     2
## GO:0016342                        CDH2/CTNNB1     2
##                    ID                             Description GeneRatio
## GO:0031625 GO:0031625        ubiquitin protein ligase binding      6/32
## GO:0044389 GO:0044389   ubiquitin-like protein ligase binding      6/32
## GO:0097718 GO:0097718      disordered domain specific binding      3/32
## GO:0043125 GO:0043125           ErbB-3 class receptor binding      2/32
## GO:0043559 GO:0043559                         insulin binding      2/32
## GO:0120283 GO:0120283 protein serine/threonine kinase binding      2/32
##              BgRatio       pvalue    p.adjust       qvalue
## GO:0031625 305/18522 1.199145e-05 0.001377779 0.0006250221
## GO:0044389 324/18522 1.688917e-05 0.001377779 0.0006250221
## GO:0097718  32/18522 2.245578e-05 0.001377779 0.0006250221
## GO:0043125   5/18522 2.882383e-05 0.001377779 0.0006250221
## GO:0043559   5/18522 2.882383e-05 0.001377779 0.0006250221
## GO:0120283   7/18522 6.039943e-05 0.002405911 0.0010914283
##                                        geneID Count
## GO:0031625 RB1/BID/TUBA1B/CDKN1B/ERBB3/SQSTM1     6
## GO:0044389 RB1/BID/TUBA1B/CDKN1B/ERBB3/SQSTM1     6
## GO:0097718                    RB1/NCOA3/GAPDH     3
## GO:0043125                       PIK3R1/ERBB3     2
## GO:0043559                       PIK3R1/IGF1R     2
## GO:0120283                         XIAP/MAPK8     2
##                    ID                                         Description
## GO:0051402 GO:0051402                            neuron apoptotic process
## GO:0030099 GO:0030099                        myeloid cell differentiation
## GO:0000082 GO:0000082               G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843                    cell cycle G1/S phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0044772 GO:0044772                 mitotic cell cycle phase transition
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051402      9/32 292/18888 9.160194e-10 1.425549e-06 8.355391e-07
## GO:0030099     10/32 439/18888 1.696073e-09 1.425549e-06 8.355391e-07
## GO:0000082      7/32 234/18888 1.058757e-07 5.932567e-05 3.477180e-05
## GO:0044843      7/32 262/18888 2.282663e-07 9.592890e-05 5.622559e-05
## GO:2000045      6/32 185/18888 5.969420e-07 1.768895e-04 1.036780e-04
## GO:0044772      8/32 451/18888 6.313724e-07 1.768895e-04 1.036780e-04
##                                                         geneID Count
## GO:0051402   RB1/XIAP/BID/CCND1/BCL2L11/ERBB3/FOXO3/G6PD/GAPDH     9
## GO:0030099 RB1/ETS1/PIK3R1/MYH9/FOXO3/GAB2/MYC/G6PD/RBM15/FASN    10
## GO:0000082              RB1/ARID1A/BID/CCND1/CDKN1B/MYC/EIF4G1     7
## GO:0044843              RB1/ARID1A/BID/CCND1/CDKN1B/MYC/EIF4G1     7
## GO:2000045                  RB1/ARID1A/BID/CCND1/CDKN1B/EIF4G1     6
## GO:0044772        RB1/ARID1A/BID/CCND1/CHEK1/CDKN1B/MYC/EIF4G1     8
##                    ID
## GO:0017053 GO:0017053
## GO:0090571 GO:0090571
## GO:0016514 GO:0016514
## GO:0061695 GO:0061695
## GO:0016235 GO:0016235
## GO:1902911 GO:1902911
##                                                               Description
## GO:0017053                                transcription repressor complex
## GO:0090571              RNA polymerase II transcription repressor complex
## GO:0016514                                                SWI/SNF complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0016235                                                      aggresome
## GO:1902911                                         protein kinase complex
##            GeneRatio   BgRatio       pvalue   p.adjust     qvalue
## GO:0017053      3/32  77/19894 0.0002550520 0.02117190 0.01203182
## GO:0090571      2/32  15/19894 0.0002597779 0.02117190 0.01203182
## GO:0016514      2/32  30/19894 0.0010601339 0.04703569 0.02673000
## GO:0061695      4/32 308/19894 0.0014393257 0.04703569 0.02673000
## GO:0016235      2/32  35/19894 0.0014428125 0.04703569 0.02673000
## GO:1902911      3/32 150/19894 0.0017752047 0.04755952 0.02702769
##                            geneID Count
## GO:0017053        CCND1/FOXO3/MYC     3
## GO:0090571              FOXO3/MYC     2
## GO:0016514             RB1/ARID1A     2
## GO:0061695 RB1/CCND1/PIK3R1/IGF1R     4
## GO:0016235            EEF2/SQSTM1     2
## GO:1902911        RB1/CCND1/IGF1R     3
##                    ID                              Description GeneRatio
## GO:0140313 GO:0140313          molecular sequestering activity      6/52
## GO:0019903 GO:0019903              protein phosphatase binding      8/52
## GO:0001221 GO:0001221        transcription coregulator binding      7/52
## GO:0019902 GO:0019902                      phosphatase binding      8/52
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     11/52
## GO:0031625 GO:0031625         ubiquitin protein ligase binding      9/52
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140313  49/18522 4.635728e-09 9.335950e-07 4.228370e-07
## GO:0019903 142/18522 5.540623e-09 9.335950e-07 4.228370e-07
## GO:0001221 114/18522 2.956987e-08 3.321682e-06 1.504432e-06
## GO:0019902 189/18522 5.195320e-08 4.377057e-06 1.982425e-06
## GO:0140297 478/18522 7.007675e-08 4.723173e-06 2.139185e-06
## GO:0031625 305/18522 1.564085e-07 8.784942e-06 3.978812e-06
##                                                                  geneID Count
## GO:0140313                          YWHAZ/CDKN1A/CAV1/STAT3/SQSTM1/LCN2     6
## GO:0019903                 MET/BCL2/CDKN1B/MAPK8/PTK2/EGFR/STAT3/CTNNB1     8
## GO:0001221                        ESR1/MYC/EZH2/ETS1/FOXO3/GATA3/CTNNB1     7
## GO:0019902                 MET/BCL2/CDKN1B/MAPK8/PTK2/EGFR/STAT3/CTNNB1     8
## GO:0140297 ESR1/BCL2/MYC/JUN/ETS1/ARID1A/YWHAZ/NCOA3/STAT3/GATA3/CTNNB1    11
## GO:0031625          BCL2/CDKN1B/JUN/BID/YWHAZ/CDKN1A/EGFR/SQSTM1/CTNNB1     9
##                    ID
## GO:0032355 GO:0032355
## GO:0048872 GO:0048872
## GO:1902893 GO:1902893
## GO:0061614 GO:0061614
## GO:0044772 GO:0044772
## GO:0043491 GO:0043491
##                                                                   Description
## GO:0032355                                              response to estradiol
## GO:0048872                                     homeostasis of number of cells
## GO:1902893                                  regulation of miRNA transcription
## GO:0061614                                                miRNA transcription
## GO:0044772                                mitotic cell cycle phase transition
## GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0032355     12/52 115/18888 2.424244e-16 7.435156e-13 3.299524e-13
## GO:0048872     15/52 322/18888 5.472674e-15 8.392346e-12 3.724299e-12
## GO:1902893      9/52  75/18888 4.794693e-13 4.161603e-10 1.846808e-10
## GO:0061614      9/52  76/18888 5.427588e-13 4.161603e-10 1.846808e-10
## GO:0044772     15/52 451/18888 7.411126e-13 4.545985e-10 2.017386e-10
## GO:0043491     13/52 299/18888 1.104312e-12 5.644877e-10 2.505046e-10
##                                                                                         geneID
## GO:0032355            ESR1/ERRFI1/IGF1R/CDKN1B/EZH2/NCOA3/EGFR/CASP3/STAT3/IGFBP2/ITGA2/CTNNB1
## GO:0048872   BAP1/G6PD/BCL2/KRAS/AKT1/BCL2L11/EZH2/XIAP/ETS1/FOXO3/AXL/CASP3/ANXA1/STAT3/GATA3
## GO:1902893                                     ESR1/NOTCH3/MYC/JUN/ETS1/FOXO3/EGFR/STAT3/GATA3
## GO:0061614                                     ESR1/NOTCH3/MYC/JUN/ETS1/FOXO3/EGFR/STAT3/GATA3
## GO:0044772 BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/CHEK1/CDKN1A/EGFR/FOXM1/CCNE2/RAD50
## GO:0043491                  ERRFI1/AKT1/IGF1R/PTEN/IRS1/FN1/AXL/PTK2/EGFR/STAT3/RET/GAB2/GATA3
##            Count
## GO:0032355    12
## GO:0048872    15
## GO:1902893     9
## GO:0061614     9
## GO:0044772    15
## GO:0043491    13
##                    ID                                       Description
## GO:0005925 GO:0005925                                    focal adhesion
## GO:0030055 GO:0030055                           cell-substrate junction
## GO:0070435 GO:0070435                                  Shc-EGFR complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0005899 GO:0005899                          insulin receptor complex
## GO:1902911 GO:1902911                            protein kinase complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0005925      9/52 421/19894 1.284721e-06 0.0001574755 9.601165e-05
## GO:0030055      9/52 431/19894 1.559164e-06 0.0001574755 9.601165e-05
## GO:0070435      2/52   2/19894 6.701178e-06 0.0003785405 2.307933e-04
## GO:0090571      3/52  15/19894 7.495851e-06 0.0003785405 2.307933e-04
## GO:0005899      2/52   4/19894 4.007244e-05 0.0014074824 8.581315e-04
## GO:1902911      5/52 150/19894 4.452637e-05 0.0014074824 8.581315e-04
##                                                       geneID Count
## GO:0005925 KRAS/SHC1/YWHAZ/PTK2/EGFR/CAV1/ANXA1/ITGA2/CTNNB1     9
## GO:0030055 KRAS/SHC1/YWHAZ/PTK2/EGFR/CAV1/ANXA1/ITGA2/CTNNB1     9
## GO:0070435                                         SHC1/EGFR     2
## GO:0090571                                  MYC/FOXO3/CTNNB1     3
## GO:0005899                                        IGF1R/IRS1     2
## GO:1902911                     CCND1/IGF1R/IRS1/CDKN1A/CCNE2     5
##                    ID                              Description GeneRatio
## GO:0106310 GO:0106310           protein serine kinase activity      5/25
## GO:0004707 GO:0004707                      MAP kinase activity      2/25
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/25
## GO:0070064 GO:0070064              proline-rich region binding      2/25
## GO:0019887 GO:0019887        protein kinase regulator activity      4/25
## GO:0019207 GO:0019207                kinase regulator activity      4/25
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0106310 363/18522 0.0001081824 0.009276705 0.003999475
## GO:0004707  16/18522 0.0002074657 0.009276705 0.003999475
## GO:0004674 427/18522 0.0002308630 0.009276705 0.003999475
## GO:0070064  17/18522 0.0002349333 0.009276705 0.003999475
## GO:0019887 232/18522 0.0002467209 0.009276705 0.003999475
## GO:0019207 270/18522 0.0004388388 0.013750282 0.005928173
##                               geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0070064                CCND1/YAP1     2
## GO:0019887   AKT1/CDKN1A/CCND1/ERBB3     4
## GO:0019207   AKT1/CDKN1A/CCND1/ERBB3     4
##                    ID                                 Description GeneRatio
## GO:0010631 GO:0010631                   epithelial cell migration      9/25
## GO:0090132 GO:0090132                        epithelium migration      9/25
## GO:0090130 GO:0090130                            tissue migration      9/25
## GO:0062197 GO:0062197        cellular response to chemical stress      8/25
## GO:0071214 GO:0071214       cellular response to abiotic stimulus      8/25
## GO:0104004 GO:0104004 cellular response to environmental stimulus      8/25
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010631 375/18888 6.722030e-10 5.409962e-07 2.240955e-07
## GO:0090132 378/18888 7.210613e-10 5.409962e-07 2.240955e-07
## GO:0090130 383/18888 8.094706e-10 5.409962e-07 2.240955e-07
## GO:0062197 311/18888 4.187089e-09 2.098778e-06 8.693718e-07
## GO:0071214 334/18888 7.318853e-09 2.302844e-06 9.539015e-07
## GO:0104004 334/18888 7.318853e-09 2.302844e-06 9.539015e-07
##                                                     geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0062197     HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1/G6PD     8
## GO:0071214     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
## GO:0104004     MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                         Description GeneRatio   BgRatio
## GO:0005925 GO:0005925                      focal adhesion      7/25 421/19894
## GO:0030055 GO:0030055             cell-substrate junction      7/25 431/19894
## GO:0005826 GO:0005826         actomyosin contractile ring      2/25   4/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane      4/25 161/19894
## GO:0070938 GO:0070938                    contractile ring      2/25  10/19894
## GO:0098562 GO:0098562        cytoplasmic side of membrane      4/25 199/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.252929e-07 4.794154e-05 2.735114e-05
## GO:0030055 7.319319e-07 4.794154e-05 2.735114e-05
## GO:0005826 9.082603e-06 3.966070e-04 2.262684e-04
## GO:0009898 4.578147e-05 1.499343e-03 8.553907e-04
## GO:0070938 6.780516e-05 1.776495e-03 1.013509e-03
## GO:0098562 1.042248e-04 2.275574e-03 1.298238e-03
##                                            geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0005826                              MYH9/ANLN     2
## GO:0009898                    MYH9/PTEN/KRAS/G6PD     4
## GO:0070938                              MYH9/ANLN     2
## GO:0098562                    MYH9/PTEN/KRAS/G6PD     4
##                    ID                              Description GeneRatio
## GO:0106310 GO:0106310           protein serine kinase activity      5/25
## GO:0004707 GO:0004707                      MAP kinase activity      2/25
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/25
## GO:0070064 GO:0070064              proline-rich region binding      2/25
## GO:0042826 GO:0042826              histone deacetylase binding      3/25
## GO:0045296 GO:0045296                         cadherin binding      4/25
##              BgRatio       pvalue   p.adjust      qvalue
## GO:0106310 363/18522 0.0001081824 0.01192286 0.004945963
## GO:0004707  16/18522 0.0002074657 0.01192286 0.004945963
## GO:0004674 427/18522 0.0002308630 0.01192286 0.004945963
## GO:0070064  17/18522 0.0002349333 0.01192286 0.004945963
## GO:0042826 128/18522 0.0006634074 0.01766587 0.007328335
## GO:0045296 333/18522 0.0009629296 0.01766587 0.007328335
##                               geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
## GO:0045296     HSPA1A/MYH9/ANLN/FASN     4
##                    ID                           Description GeneRatio   BgRatio
## GO:0010631 GO:0010631             epithelial cell migration      9/25 375/18888
## GO:0090132 GO:0090132                  epithelium migration      9/25 378/18888
## GO:0090130 GO:0090130                      tissue migration      9/25 383/18888
## GO:0030099 GO:0030099          myeloid cell differentiation      9/25 439/18888
## GO:0062197 GO:0062197  cellular response to chemical stress      8/25 311/18888
## GO:0071214 GO:0071214 cellular response to abiotic stimulus      8/25 334/18888
##                  pvalue     p.adjust       qvalue
## GO:0010631 6.722030e-10 5.415358e-07 2.272198e-07
## GO:0090132 7.210613e-10 5.415358e-07 2.272198e-07
## GO:0090130 8.094706e-10 5.415358e-07 2.272198e-07
## GO:0030099 2.679241e-09 1.344309e-06 5.640507e-07
## GO:0062197 4.187089e-09 1.680697e-06 7.051939e-07
## GO:0071214 7.318853e-09 2.016998e-06 8.463004e-07
##                                                        geneID Count
## GO:0010631    AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090132    AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0090130    AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ANLN/ITGA2     9
## GO:0030099 HSPA1A/MTOR/MYH9/FOXO3/CASP8/ETS1/STAT5A/G6PD/FASN     9
## GO:0062197        HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1/G6PD     8
## GO:0071214        MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2     8
##                    ID                         Description GeneRatio   BgRatio
## GO:0005925 GO:0005925                      focal adhesion      7/25 421/19894
## GO:0030055 GO:0030055             cell-substrate junction      7/25 431/19894
## GO:0005826 GO:0005826         actomyosin contractile ring      2/25   4/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane      4/25 161/19894
## GO:0070938 GO:0070938                    contractile ring      2/25  10/19894
## GO:0098562 GO:0098562        cytoplasmic side of membrane      4/25 199/19894
##                  pvalue     p.adjust       qvalue
## GO:0005925 6.252929e-07 4.757557e-05 2.696591e-05
## GO:0030055 7.319319e-07 4.757557e-05 2.696591e-05
## GO:0005826 9.082603e-06 3.935795e-04 2.230815e-04
## GO:0009898 4.578147e-05 1.487898e-03 8.433429e-04
## GO:0070938 6.780516e-05 1.762934e-03 9.992340e-04
## GO:0098562 1.042248e-04 2.258203e-03 1.279953e-03
##                                            geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/MAPK1/ITGA2/TGM2     7
## GO:0005826                              MYH9/ANLN     2
## GO:0009898                    MYH9/PTEN/KRAS/G6PD     4
## GO:0070938                              MYH9/ANLN     2
## GO:0098562                    MYH9/PTEN/KRAS/G6PD     4
##                    ID                              Description GeneRatio
## GO:0031625 GO:0031625         ubiquitin protein ligase binding      6/29
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      7/29
## GO:0044389 GO:0044389    ubiquitin-like protein ligase binding      6/29
## GO:0097718 GO:0097718       disordered domain specific binding      3/29
## GO:0043559 GO:0043559                          insulin binding      2/29
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/29
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0031625 305/18522 6.552559e-06 0.0005737005 0.0002597399
## GO:0140297 478/18522 6.958424e-06 0.0005737005 0.0002597399
## GO:0044389 324/18522 9.253234e-06 0.0005737005 0.0002597399
## GO:0097718  32/18522 1.660139e-05 0.0007719648 0.0003495030
## GO:0043559   5/18522 2.360135e-05 0.0008779703 0.0003974965
## GO:0120283   7/18522 4.946657e-05 0.0015293667 0.0006924128
##                                           geneID Count
## GO:0031625    RB1/BID/CDKN1A/CASP8/TUBA1B/CTNNB1     6
## GO:0140297 RB1/ETS1/ARID1A/NCOA3/YAP1/CTNNB1/VHL     7
## GO:0044389    RB1/BID/CDKN1A/CASP8/TUBA1B/CTNNB1     6
## GO:0097718                      RB1/NCOA3/CTNNB1     3
## GO:0043559                          PIK3R1/IGF1R     2
## GO:0120283                            XIAP/MAPK8     2
##                    ID                                       Description
## GO:0051402 GO:0051402                          neuron apoptotic process
## GO:0030099 GO:0030099                      myeloid cell differentiation
## GO:0071214 GO:0071214             cellular response to abiotic stimulus
## GO:0104004 GO:0104004       cellular response to environmental stimulus
## GO:1901990 GO:1901990 regulation of mitotic cell cycle phase transition
## GO:0002573 GO:0002573                 myeloid leukocyte differentiation
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051402      8/29 292/18888 9.600031e-09 1.111329e-05 5.174450e-06
## GO:0030099      9/29 439/18888 1.209281e-08 1.111329e-05 5.174450e-06
## GO:0071214      8/29 334/18888 2.730658e-08 1.254737e-05 5.842171e-06
## GO:0104004      8/29 334/18888 2.730658e-08 1.254737e-05 5.842171e-06
## GO:1901990      8/29 356/18888 4.473172e-08 1.644338e-05 7.656186e-06
## GO:0002573      7/29 239/18888 5.856733e-08 1.794113e-05 8.353551e-06
##                                                       geneID Count
## GO:0051402         RB1/XIAP/BID/FOXO3/ATM/CASP8/CCND1/CTNNB1     8
## GO:0030099 RB1/ETS1/MYH9/FOXO3/CASP8/PIK3R1/GAB2/FASN/CTNNB1     9
## GO:0071214    MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:0104004    MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1     8
## GO:1901990        RB1/ARID1A/BID/CDKN1A/ATM/CCND1/CHEK1/ANLN     8
## GO:0002573            RB1/MYH9/CASP8/PIK3R1/GAB2/FASN/CTNNB1     7
##                    ID
## GO:0005826 GO:0005826
## GO:1902911 GO:1902911
## GO:0000307 GO:0000307
## GO:0061695 GO:0061695
## GO:0070938 GO:0070938
## GO:0017053 GO:0017053
##                                                               Description
## GO:0005826                                    actomyosin contractile ring
## GO:1902911                                         protein kinase complex
## GO:0000307             cyclin-dependent protein kinase holoenzyme complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0070938                                               contractile ring
## GO:0017053                                transcription repressor complex
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0005826      2/29   4/19894 1.228849e-05 0.002150486 0.001164173
## GO:1902911      4/29 150/19894 6.367879e-05 0.003208261 0.001736803
## GO:0000307      3/29  56/19894 7.329106e-05 0.003208261 0.001736803
## GO:0061695      5/29 308/19894 7.536722e-05 0.003208261 0.001736803
## GO:0070938      2/29  10/19894 9.166460e-05 0.003208261 0.001736803
## GO:0017053      3/29  77/19894 1.894704e-04 0.004993295 0.002703137
##                                   geneID Count
## GO:0005826                     MYH9/ANLN     2
## GO:1902911        RB1/CDKN1A/CCND1/IGF1R     4
## GO:0000307              RB1/CDKN1A/CCND1     3
## GO:0061695 RB1/CDKN1A/CCND1/PIK3R1/IGF1R     5
## GO:0070938                     MYH9/ANLN     2
## GO:0017053            FOXO3/CCND1/CTNNB1     3
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, Bicluster 1 of 1")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, Bicluster 1 of 2")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, Bicluster 2 of 2")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, Bicluster 1 of 3")

barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, Bicluster 2 of 3")

barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, Bicluster 3 of 3")

barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, Bicluster 1 of 5")

barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, Bicluster 2 of 5")

barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, Bicluster 3 of 5")

barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, Bicluster 4 of 5")

barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, Bicluster 5 of 5")

barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, Bicluster 1 of 10")

barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, Bicluster 2 of 10")

barplot(ego_MF[[14]], title = "enrichGO, Molecular Function, Bicluster 3 of 10")

barplot(ego_MF[[15]], title = "enrichGO, Molecular Function, Bicluster 4 of 10")

barplot(ego_MF[[16]], title = "enrichGO, Molecular Function, Bicluster 5 of 10")

barplot(ego_MF[[17]], title = "enrichGO, Molecular Function, Bicluster 6 of 10")

barplot(ego_MF[[18]], title = "enrichGO, Molecular Function, Bicluster 7 of 10")

barplot(ego_MF[[19]], title = "enrichGO, Molecular Function, Bicluster 8 of 10")

barplot(ego_MF[[20]], title = "enrichGO, Molecular Function, Bicluster 9 of 10")

barplot(ego_MF[[21]], title = "enrichGO, Molecular Function, Bicluster 10 of 10")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, Bicluster 1 of 1")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, Bicluster 1 of 2")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, Bicluster 2 of 2")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, Bicluster 1 of 3")

barplot(ego_BP[[5]], title = "enrichGO, Biological Process, Bicluster 2 of 3")

barplot(ego_BP[[6]], title = "enrichGO, Biological Process, Bicluster 3 of 3")

barplot(ego_BP[[7]], title = "enrichGO, Biological Process, Bicluster 1 of 5")

barplot(ego_BP[[8]], title = "enrichGO, Biological Process, Bicluster 2 of 5")

barplot(ego_BP[[9]], title = "enrichGO, Biological Process, Bicluster 3 of 5")

barplot(ego_BP[[10]], title = "enrichGO, Biological Process, Bicluster 4 of 5")

barplot(ego_BP[[11]], title = "enrichGO, Biological Process, Bicluster 5 of 5")

barplot(ego_BP[[12]], title = "enrichGO, Biological Process, Bicluster 1 of 10")

barplot(ego_BP[[13]], title = "enrichGO, Biological Process, Bicluster 2 of 10")

barplot(ego_BP[[14]], title = "enrichGO, Biological Process, Bicluster 3 of 10")

barplot(ego_BP[[15]], title = "enrichGO, Biological Process, Bicluster 4 of 10")

barplot(ego_BP[[16]], title = "enrichGO, Biological Process, Bicluster 5 of 10")

barplot(ego_BP[[17]], title = "enrichGO, Biological Process, Bicluster 6 of 10")

barplot(ego_BP[[18]], title = "enrichGO, Biological Process, Bicluster 7 of 10")

barplot(ego_BP[[19]], title = "enrichGO, Biological Process, Bicluster 8 of 10")

barplot(ego_BP[[20]], title = "enrichGO, Biological Process, Bicluster 9 of 10")

barplot(ego_BP[[21]], title = "enrichGO, Biological Process, Bicluster 10 of 10")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, Bicluster 1 of 1")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, Bicluster 1 of 2")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, Bicluster 2 of 2")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, Bicluster 1 of 3")

barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, Bicluster 2 of 3")

barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, Bicluster 3 of 3")

barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, Bicluster 1 of 5")

barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, Bicluster 2 of 5")

barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, Bicluster 3 of 5")

barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, Bicluster 4 of 5")

barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, Bicluster 5 of 5")

barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, Bicluster 1 of 10")

barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, Bicluster 2 of 10")

barplot(ego_CC[[14]], title = "enrichGO, Cellular Component, Bicluster 3 of 10")

barplot(ego_CC[[15]], title = "enrichGO, Cellular Component, Bicluster 4 of 10")

barplot(ego_CC[[16]], title = "enrichGO, Cellular Component, Bicluster 5 of 10")

barplot(ego_CC[[17]], title = "enrichGO, Cellular Component, Bicluster 6 of 10")

barplot(ego_CC[[18]], title = "enrichGO, Cellular Component, Bicluster 7 of 10")

barplot(ego_CC[[19]], title = "enrichGO, Cellular Component, Bicluster 8 of 10")

barplot(ego_CC[[20]], title = "enrichGO, Cellular Component, Bicluster 9 of 10")

barplot(ego_CC[[21]], title = "enrichGO, Cellular Component, Bicluster 10 of 10")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 1")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 2")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 2")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 3")

goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 3")

goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, Bicluster 3 of 3")

goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 5")

goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 5")

goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, Bicluster 3 of 5")

goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, Bicluster 4 of 5")

goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, Bicluster 5 of 5")

goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 10")

goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 10")

goplot(ego_MF[[14]]) + labs(title = "enrichGO, Molecular Function, Bicluster 3 of 10")

goplot(ego_MF[[15]]) + labs(title = "enrichGO, Molecular Function, Bicluster 4 of 10")

goplot(ego_MF[[16]]) + labs(title = "enrichGO, Molecular Function, Bicluster 5 of 10")

goplot(ego_MF[[17]]) + labs(title = "enrichGO, Molecular Function, Bicluster 6 of 10")

goplot(ego_MF[[18]]) + labs(title = "enrichGO, Molecular Function, Bicluster 7 of 10")

goplot(ego_MF[[19]]) + labs(title = "enrichGO, Molecular Function, Bicluster 8 of 10")

goplot(ego_MF[[20]]) + labs(title = "enrichGO, Molecular Function, Bicluster 9 of 10")

goplot(ego_MF[[21]]) + labs(title = "enrichGO, Molecular Function, Bicluster 10 of 10")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 1")

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 2")

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 2")

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 3")

goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 3")

goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, Bicluster 3 of 3")
## Warning: ggrepel: 22 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 5")

goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 5")

goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, Bicluster 3 of 5")

goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, Bicluster 4 of 5")
## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, Bicluster 5 of 5")
## Warning: ggrepel: 7 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 10")

goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 10")

goplot(ego_BP[[14]]) + labs(title = "enrichGO, Biological Process, Bicluster 3 of 10")

goplot(ego_BP[[15]]) + labs(title = "enrichGO, Biological Process, Bicluster 4 of 10")

goplot(ego_BP[[16]]) + labs(title = "enrichGO, Biological Process, Bicluster 5 of 10")

goplot(ego_BP[[17]]) + labs(title = "enrichGO, Biological Process, Bicluster 6 of 10")

goplot(ego_BP[[18]]) + labs(title = "enrichGO, Biological Process, Bicluster 7 of 10")
## Warning: ggrepel: 22 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[19]]) + labs(title = "enrichGO, Biological Process, Bicluster 8 of 10")

goplot(ego_BP[[20]]) + labs(title = "enrichGO, Biological Process, Bicluster 9 of 10")

goplot(ego_BP[[21]]) + labs(title = "enrichGO, Biological Process, Bicluster 10 of 10")

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 1")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 2")

goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 2")

goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 3")

goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 3")

goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, Bicluster 3 of 3")

goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 5")

goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 5")

goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, Bicluster 3 of 5")

goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, Bicluster 4 of 5")

goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, Bicluster 5 of 5")

goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 10")

goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 10")

goplot(ego_CC[[14]]) + labs(title = "enrichGO, Cellular Component, Bicluster 3 of 10")

goplot(ego_CC[[15]]) + labs(title = "enrichGO, Cellular Component, Bicluster 4 of 10")

goplot(ego_CC[[16]]) + labs(title = "enrichGO, Cellular Component, Bicluster 5 of 10")

goplot(ego_CC[[17]]) + labs(title = "enrichGO, Cellular Component, Bicluster 6 of 10")

goplot(ego_CC[[18]]) + labs(title = "enrichGO, Cellular Component, Bicluster 7 of 10")

goplot(ego_CC[[19]]) + labs(title = "enrichGO, Cellular Component, Bicluster 8 of 10")

goplot(ego_CC[[20]]) + labs(title = "enrichGO, Cellular Component, Bicluster 9 of 10")

goplot(ego_CC[[21]]) + labs(title = "enrichGO, Cellular Component, Bicluster 10 of 10")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_fabia_top_5_percent.rds")